/*\r
* Jalview - A Sequence Alignment Editor and Viewer\r
- * Copyright (C) 2005 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
+ * Copyright (C) 2007 AM Waterhouse, J Procter, G Barton, M Clamp, S Searle\r
*\r
* This program is free software; you can redistribute it and/or\r
* modify it under the terms of the GNU General Public License\r
\r
package jalview.appletgui;\r
\r
-import jalview.jbappletgui.GAlignFrame;\r
-import jalview.schemes.*;\r
-import jalview.datamodel.*;\r
-import jalview.analysis.*;\r
-import jalview.io.*;\r
+import java.io.*;\r
+import java.net.*;\r
+import java.util.*;\r
+\r
import java.awt.*;\r
import java.awt.event.*;\r
-import java.util.*;\r
-import java.io.InputStreamReader;\r
-import java.io.BufferedReader;\r
\r
-public class AlignFrame\r
- extends GAlignFrame\r
-{\r
- final AlignmentPanel alignPanel;\r
- final AlignViewport viewport;\r
- public static final int NEW_WINDOW_WIDTH = 700;\r
- public static final int NEW_WINDOW_HEIGHT = 500;\r
- jalview.bin.JalviewLite applet;\r
+import jalview.analysis.*;\r
+import jalview.commands.*;\r
+import jalview.datamodel.*;\r
+import jalview.io.*;\r
+import jalview.schemes.*;\r
+\r
+public class AlignFrame\r
+ extends Frame implements ActionListener,\r
+ ItemListener, KeyListener, MouseListener\r
+{\r
+ public AlignmentPanel alignPanel;\r
+ public AlignViewport viewport;\r
+ int DEFAULT_WIDTH = 700;\r
+ int DEFAULT_HEIGHT = 500;\r
+\r
+ String jalviewServletURL;\r
+\r
+ public AlignFrame(AlignmentI al,\r
+ jalview.bin.JalviewLite applet,\r
+ String title,\r
+ boolean embedded)\r
+ {\r
+\r
+ if (applet != null)\r
+ {\r
+ jalviewServletURL = applet.getParameter("APPLICATION_URL");\r
+ }\r
+\r
+ try\r
+ {\r
+ jbInit();\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ viewport = new AlignViewport(al, applet);\r
+ alignPanel = new AlignmentPanel(this, viewport);\r
+\r
+ viewport.updateConservation(alignPanel);\r
+ viewport.updateConsensus(alignPanel);\r
+\r
+ annotationPanelMenuItem.setState(viewport.showAnnotation);\r
+\r
+ seqLimits.setState(viewport.showJVSuffix);\r
+\r
+ if (applet != null)\r
+ {\r
+ String param = applet.getParameter("sortBy");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("Id"))\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (param.equalsIgnoreCase("Pairwise Identity"))\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ }\r
+\r
+ param = applet.getParameter("wrap");\r
+ if (param != null)\r
+ {\r
+ if (param.equalsIgnoreCase("true"))\r
+ {\r
+ wrapMenuItem.setState(true);\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ }\r
+\r
+ try\r
+ {\r
+ param = applet.getParameter("windowWidth");\r
+ if (param != null)\r
+ {\r
+ int width = Integer.parseInt(param);\r
+ DEFAULT_WIDTH = width;\r
+ }\r
+ param = applet.getParameter("windowHeight");\r
+ if (param != null)\r
+ {\r
+ int height = Integer.parseInt(param);\r
+ DEFAULT_HEIGHT = height;\r
+ }\r
+ }\r
+ catch (Exception ex)\r
+ {}\r
+\r
+ }\r
+\r
+ //Some JVMS send keyevents to Top frame or lowest panel,\r
+ //Havent worked out why yet. So add to both this frame and seqCanvas for now\r
+ this.addKeyListener(this);\r
+ alignPanel.seqPanel.seqCanvas.addKeyListener(this);\r
+ alignPanel.idPanel.idCanvas.addKeyListener(this);\r
+ alignPanel.scalePanel.addKeyListener(this);\r
+ alignPanel.annotationPanel.addKeyListener(this);\r
+\r
+ if (embedded)\r
+ {\r
+ setEmbedded();\r
+ }\r
+ else\r
+ {\r
+ add(alignPanel, BorderLayout.CENTER);\r
+ jalview.bin.JalviewLite.addFrame(this, title, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
+ }\r
+ alignPanel.validate();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public AlignViewport getAlignViewport()\r
+ {\r
+ return viewport;\r
+ }\r
+\r
+ public SeqCanvas getSeqcanvas()\r
+ {\r
+ return alignPanel.seqPanel.seqCanvas;\r
+ }\r
+\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param String DOCUMENT ME!\r
+ */\r
+\r
+ public void parseFeaturesFile(String file, String type)\r
+ {\r
+ Hashtable featureLinks = new Hashtable();\r
+ boolean featuresFile = false;\r
+ try\r
+ {\r
+ featuresFile = new jalview.io.FeaturesFile(file,\r
+ type).parse(viewport.alignment,\r
+ alignPanel.seqPanel.seqCanvas.\r
+ getFeatureRenderer().featureColours,\r
+ featureLinks,\r
+ true);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+\r
+ if (featuresFile)\r
+ {\r
+ if (featureLinks.size() > 0)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas\r
+ .getFeatureRenderer().featureLinks = featureLinks;\r
+ }\r
+ viewport.showSequenceFeatures = true;\r
+ sequenceFeatures.setState(true);\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ }\r
+\r
+ public void keyPressed(KeyEvent evt)\r
+ {\r
+ if (viewport.cursorMode &&\r
+ ( (evt.getKeyCode() >= KeyEvent.VK_0 &&\r
+ evt.getKeyCode() <= KeyEvent.VK_9)\r
+ ||\r
+ (evt.getKeyCode() >= KeyEvent.VK_NUMPAD0 &&\r
+ evt.getKeyCode() <= KeyEvent.VK_NUMPAD9)\r
+ )\r
+ && Character.isDigit(evt.getKeyChar()))\r
+ alignPanel.seqPanel.numberPressed(evt.getKeyChar());\r
+\r
+\r
+ switch (evt.getKeyCode())\r
+ {\r
+ case 27: // escape key\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ break;\r
+ case KeyEvent.VK_X:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_C:\r
+ if (viewport.cursorMode && !evt.isControlDown())\r
+ {\r
+ alignPanel.seqPanel.setCursorColumn();\r
+ }\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_V:\r
+ if (evt.isControlDown())\r
+ {\r
+ paste(evt.isShiftDown());\r
+ }\r
+ break;\r
+ case KeyEvent.VK_A:\r
+ if (evt.isControlDown() || evt.isMetaDown())\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_DOWN:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, 1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_UP:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.moveCursor(0, -1);\r
+ }\r
+ else\r
+ {\r
+ moveSelectedSequences(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_LEFT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(false,\r
+ alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor( -1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_RIGHT:\r
+ if (evt.isAltDown() || !viewport.cursorMode)\r
+ slideSequences(true,\r
+ alignPanel.seqPanel.getKeyboardNo1());\r
+ else\r
+ alignPanel.seqPanel.moveCursor( 1, 0);\r
+ break;\r
+\r
+ case KeyEvent.VK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.insertGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown()\r
+ || evt.isAltDown()\r
+ );\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_DELETE:\r
+ case KeyEvent.VK_BACK_SPACE:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.deleteGapAtCursor(evt.isControlDown()\r
+ || evt.isShiftDown()\r
+ || evt.isAltDown());\r
+ }\r
+ else\r
+ {\r
+ cut_actionPerformed();\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_S:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRow();\r
+ }\r
+ break;\r
+ case KeyEvent.VK_P:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorPosition();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_ENTER:\r
+ case KeyEvent.VK_COMMA:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setCursorRowAndColumn();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Q:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(true);\r
+ }\r
+ break;\r
+ case KeyEvent.VK_M:\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.setSelectionAreaAtCursor(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F2:\r
+ viewport.cursorMode = !viewport.cursorMode;\r
+ statusBar.setText("Keyboard editing mode is " +\r
+ (viewport.cursorMode ? "on" : "off"));\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.seqCanvas.cursorX = viewport.startRes;\r
+ alignPanel.seqPanel.seqCanvas.cursorY = viewport.startSeq;\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_F:\r
+ if (evt.isControlDown())\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_H:\r
+ {\r
+ boolean toggleSeqs = !evt.isControlDown();\r
+ boolean toggleCols = !evt.isShiftDown();\r
+ boolean hide = false;\r
+ SequenceGroup sg = viewport.getSelectionGroup();\r
+\r
+ if (toggleSeqs)\r
+ {\r
+ if (sg != null && sg.getSize() != viewport.alignment.getHeight())\r
+ {\r
+ hide = true;\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (! (toggleCols && viewport.colSel.getSelected().size() > 0))\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ }\r
+\r
+ if (toggleCols)\r
+ {\r
+ if (viewport.colSel.getSelected().size() > 0)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ if (!toggleSeqs)\r
+ {\r
+ viewport.selectionGroup = sg;\r
+ }\r
+ }\r
+ else if (!hide)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ }\r
+ }\r
+ break;\r
+ }\r
+\r
+ case KeyEvent.VK_PAGE_UP:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(true);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes,\r
+ viewport.startSeq\r
+ - viewport.endSeq + viewport.startSeq);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_PAGE_DOWN:\r
+ if (viewport.wrapAlignment)\r
+ {\r
+ alignPanel.scrollUp(false);\r
+ }\r
+ else\r
+ {\r
+ alignPanel.setScrollValues(viewport.startRes,\r
+ viewport.startSeq\r
+ + viewport.endSeq - viewport.startSeq);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Z:\r
+ if (evt.isControlDown())\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_Y:\r
+ if (evt.isControlDown())\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_L:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_R:\r
+ if (evt.isControlDown())\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_E:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isShiftDown())\r
+ {\r
+ this.removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ break;\r
+ case KeyEvent.VK_I:\r
+ if (evt.isControlDown())\r
+ {\r
+ if (evt.isAltDown())\r
+ {\r
+ viewport.invertColumnSelection();\r
+ }\r
+ else\r
+ {\r
+ this.invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_U:\r
+ if (evt.isControlDown())\r
+ {\r
+ this.deleteGroups_actionPerformed();\r
+ }\r
+ break;\r
+\r
+ case KeyEvent.VK_T:\r
+ if (evt.isControlDown())\r
+ {\r
+ newView();\r
+ }\r
+ break;\r
+\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void keyReleased(KeyEvent evt)\r
+ {}\r
+\r
+ public void keyTyped(KeyEvent evt)\r
+ {}\r
+\r
+ public void itemStateChanged(ItemEvent evt)\r
+ {\r
+ if (evt.getSource() == colourTextMenuItem)\r
+ {\r
+ colourTextMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == wrapMenuItem)\r
+ {\r
+ wrapMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == scaleAbove)\r
+ {\r
+ viewport.setScaleAboveWrapped(scaleAbove.getState());\r
+ }\r
+ else if (evt.getSource() == scaleLeft)\r
+ {\r
+ viewport.setScaleLeftWrapped(scaleLeft.getState());\r
+ }\r
+ else if (evt.getSource() == scaleRight)\r
+ {\r
+ viewport.setScaleRightWrapped(scaleRight.getState());\r
+ }\r
+ else if (evt.getSource() == seqLimits)\r
+ {\r
+ seqLimits_itemStateChanged();\r
+ }\r
+ else if (evt.getSource() == viewBoxesMenuItem)\r
+ {\r
+ viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == viewTextMenuItem)\r
+ {\r
+ viewport.setShowText(viewTextMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == renderGapsMenuItem)\r
+ {\r
+ viewport.setRenderGaps(renderGapsMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == annotationPanelMenuItem)\r
+ {\r
+ viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
+ alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ }\r
+ else if (evt.getSource() == sequenceFeatures)\r
+ {\r
+ viewport.showSequenceFeatures(sequenceFeatures.getState());\r
+ alignPanel.seqPanel.seqCanvas.repaint();\r
+ }\r
+ else if (evt.getSource() == conservationMenuItem)\r
+ {\r
+ conservationMenuItem_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == abovePIDThreshold)\r
+ {\r
+ abovePIDThreshold_actionPerformed();\r
+ }\r
+ else if (evt.getSource() == applyToAllGroups)\r
+ {\r
+ viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
+ }\r
+ else if (evt.getSource() == autoCalculate)\r
+ {\r
+ viewport.autocalculateConsensus = autoCalculate.getState();\r
+ }\r
+\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ public void actionPerformed(ActionEvent evt)\r
+ {\r
+ Object source = evt.getSource();\r
+\r
+ if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == loadTree)\r
+ {\r
+ loadTree_actionPerformed();\r
+ }\r
+ else if (source == loadApplication)\r
+ {\r
+ launchFullApplication();\r
+ }\r
+ else if (source == loadAnnotations)\r
+ {\r
+ loadAnnotations();\r
+ }\r
+ else if (source == outputAnnotations)\r
+ {\r
+ outputAnnotations(true);\r
+ }\r
+ else if (source == outputFeatures)\r
+ {\r
+ outputFeatures(true, "Jalview");\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == inputText)\r
+ {\r
+ inputText_actionPerformed();\r
+ }\r
+ else if (source == closeMenuItem)\r
+ {\r
+ closeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == undoMenuItem)\r
+ {\r
+ undoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == redoMenuItem)\r
+ {\r
+ redoMenuItem_actionPerformed();\r
+ }\r
+ else if (source == copy)\r
+ {\r
+ copy_actionPerformed();\r
+ }\r
+ else if (source == pasteNew)\r
+ {\r
+ pasteNew_actionPerformed();\r
+ }\r
+ else if (source == pasteThis)\r
+ {\r
+ pasteThis_actionPerformed();\r
+ }\r
+ else if (source == cut)\r
+ {\r
+ cut_actionPerformed();\r
+ }\r
+ else if (source == delete)\r
+ {\r
+ delete_actionPerformed();\r
+ }\r
+ else if (source == deleteGroups)\r
+ {\r
+ deleteGroups_actionPerformed();\r
+ }\r
+ else if (source == selectAllSequenceMenuItem)\r
+ {\r
+ selectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == deselectAllSequenceMenuItem)\r
+ {\r
+ deselectAllSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertSequenceMenuItem)\r
+ {\r
+ invertSequenceMenuItem_actionPerformed();\r
+ }\r
+ else if (source == invertColSel)\r
+ {\r
+ viewport.invertColumnSelection();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == remove2LeftMenuItem)\r
+ {\r
+ trimAlignment(true);\r
+ }\r
+ else if (source == remove2RightMenuItem)\r
+ {\r
+ trimAlignment(false);\r
+ }\r
+ else if (source == removeGappedColumnMenuItem)\r
+ {\r
+ removeGappedColumnMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeAllGapsMenuItem)\r
+ {\r
+ removeAllGapsMenuItem_actionPerformed();\r
+ }\r
+ else if (source == findMenuItem)\r
+ {\r
+ findMenuItem_actionPerformed();\r
+ }\r
+ else if (source == font)\r
+ {\r
+ new FontChooser(alignPanel);\r
+ }\r
+ else if (source == newView)\r
+ {\r
+ newView();\r
+ }\r
+ else if (source == showColumns)\r
+ {\r
+ viewport.showAllHiddenColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == showSeqs)\r
+ {\r
+ viewport.showAllHiddenSeqs();\r
+ }\r
+ else if (source == hideColumns)\r
+ {\r
+ viewport.hideSelectedColumns();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+ else if (source == hideSequences && viewport.getSelectionGroup() != null)\r
+ {\r
+ viewport.hideAllSelectedSeqs();\r
+ }\r
+ else if (source == featureSettings)\r
+ {\r
+ new FeatureSettings(alignPanel);\r
+ }\r
+ else if (source == overviewMenuItem)\r
+ {\r
+ overviewMenuItem_actionPerformed();\r
+ }\r
+ else if (source == noColourmenuItem)\r
+ {\r
+ changeColour(null);\r
+ }\r
+ else if (source == clustalColour)\r
+ {\r
+ abovePIDThreshold.setState(false);\r
+ changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
+ viewport.alignment.getWidth()));\r
+ }\r
+ else if (source == zappoColour)\r
+ {\r
+ changeColour(new ZappoColourScheme());\r
+ }\r
+ else if (source == taylorColour)\r
+ {\r
+ changeColour(new TaylorColourScheme());\r
+ }\r
+ else if (source == hydrophobicityColour)\r
+ {\r
+ changeColour(new HydrophobicColourScheme());\r
+ }\r
+ else if (source == helixColour)\r
+ {\r
+ changeColour(new HelixColourScheme());\r
+ }\r
+ else if (source == strandColour)\r
+ {\r
+ changeColour(new StrandColourScheme());\r
+ }\r
+ else if (source == turnColour)\r
+ {\r
+ changeColour(new TurnColourScheme());\r
+ }\r
+ else if (source == buriedColour)\r
+ {\r
+ changeColour(new BuriedColourScheme());\r
+ }\r
+ else if (source == nucleotideColour)\r
+ {\r
+ changeColour(new NucleotideColourScheme());\r
+ }\r
+ else if (source == modifyPID)\r
+ {\r
+ modifyPID_actionPerformed();\r
+ }\r
+ else if (source == modifyConservation)\r
+ {\r
+ modifyConservation_actionPerformed();\r
+ }\r
+ else if (source == userDefinedColour)\r
+ {\r
+ new UserDefinedColours(alignPanel, null);\r
+ }\r
+ else if (source == PIDColour)\r
+ {\r
+ changeColour(new PIDColourScheme());\r
+ }\r
+ else if (source == BLOSUM62Colour)\r
+ {\r
+ changeColour(new Blosum62ColourScheme());\r
+ }\r
+ else if (source == annotationColour)\r
+ {\r
+ new AnnotationColourChooser(viewport, alignPanel);\r
+ }\r
+ else if (source == sortPairwiseMenuItem)\r
+ {\r
+ sortPairwiseMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortIDMenuItem)\r
+ {\r
+ sortIDMenuItem_actionPerformed();\r
+ }\r
+ else if (source == sortGroupMenuItem)\r
+ {\r
+ sortGroupMenuItem_actionPerformed();\r
+ }\r
+ else if (source == removeRedundancyMenuItem)\r
+ {\r
+ removeRedundancyMenuItem_actionPerformed();\r
+ }\r
+ else if (source == pairwiseAlignmentMenuItem)\r
+ {\r
+ pairwiseAlignmentMenuItem_actionPerformed();\r
+ }\r
+ else if (source == PCAMenuItem)\r
+ {\r
+ PCAMenuItem_actionPerformed();\r
+ }\r
+ else if (source == averageDistanceTreeMenuItem)\r
+ {\r
+ averageDistanceTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == neighbourTreeMenuItem)\r
+ {\r
+ neighbourTreeMenuItem_actionPerformed();\r
+ }\r
+ else if (source == njTreeBlosumMenuItem)\r
+ {\r
+ njTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == avDistanceTreeBlosumMenuItem)\r
+ {\r
+ avTreeBlosumMenuItem_actionPerformed();\r
+ }\r
+ else if (source == documentation)\r
+ {\r
+ documentation_actionPerformed();\r
+ }\r
+ else if (source == about)\r
+ {\r
+ about_actionPerformed();\r
+ }\r
+\r
+ }\r
+\r
+ public void inputText_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
+ }\r
+\r
+ protected void outputText_actionPerformed(ActionEvent e)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Alignment output - " + e.getActionCommand(),\r
+ 600, 500);\r
+ cap.setText(new AppletFormatAdapter().formatSequences(e.getActionCommand(),\r
+ viewport.getAlignment(),\r
+ viewport.showJVSuffix));\r
+ }\r
+\r
+ public void loadAnnotations()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your features / annotations file here.");\r
+ cap.setAnnotationImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Annotations ", 400, 300);\r
+\r
+ }\r
+\r
+ public String outputAnnotations(boolean displayTextbox)\r
+ {\r
+ String annotation = new AnnotationFile().printAnnotations(\r
+ viewport.showAnnotation ? viewport.alignment.getAlignmentAnnotation() : null,\r
+ viewport.alignment.getGroups(),\r
+ ((Alignment)viewport.alignment).alignmentProperties);\r
+\r
+ if (displayTextbox)\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Annotations",\r
+ 600, 500);\r
+ cap.setText(annotation);\r
+ }\r
\r
+ return annotation;\r
+ }\r
\r
- public AlignFrame(AlignmentI al, jalview.bin.JalviewLite applet)\r
+ public String outputFeatures(boolean displayTextbox, String format)\r
{\r
- this.applet = applet;\r
- viewport = new AlignViewport(al, applet);\r
- alignPanel = new AlignmentPanel(this, viewport);\r
- add(alignPanel);\r
- alignPanel.validate();\r
+ String features;\r
+ if (format.equalsIgnoreCase("Jalview"))\r
+ {\r
+ features = new FeaturesFile().printJalviewFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ }\r
+ else\r
+ {\r
+ features = new FeaturesFile().printGFFFormat(\r
+ viewport.alignment.getSequencesArray(),\r
+ viewport.featuresDisplayed);\r
+ }\r
\r
- if(applet!=null)\r
+ if (displayTextbox)\r
{\r
- String treeFile = applet.getParameter("treeFile");\r
- if (treeFile != null)\r
- {\r
- try\r
- {\r
- treeFile = treeFile;\r
- jalview.io.NewickFile fin = new jalview.io.NewickFile(applet.\r
- getCodeBase() + treeFile, "URL");\r
- fin.parse();\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(false, this);\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame,\r
+ "Features",\r
+ 600, 500);\r
\r
- if (fin.getTree() != null)\r
- {\r
- TreePanel tp = null;\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- fin, "FromFile", applet.getCodeBase() + treeFile);\r
- jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
- addTreeMenuItem(tp, treeFile);\r
- }\r
- }\r
- catch (Exception ex)\r
- {\r
- ex.printStackTrace();\r
- }\r
- }\r
+ cap.setText(features);\r
+ }\r
\r
- String param = applet.getParameter("sortBy");\r
- if (param != null)\r
- {\r
- if (param.equalsIgnoreCase("Id"))\r
- sortIDMenuItem_actionPerformed(null);\r
- else if (param.equalsIgnoreCase("Pairwise Identity"))\r
- sortPairwiseMenuItem_actionPerformed(null);\r
- }\r
+ return features;\r
+ }\r
+\r
+ void launchFullApplication()\r
+ {\r
+ StringBuffer url = new StringBuffer(jalviewServletURL);\r
+\r
+ url.append("?open=" +\r
+ appendProtocol(viewport.applet.getParameter("file")));\r
+\r
+ if (viewport.applet.getParameter("features") != null)\r
+ {\r
+ url.append("&features=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("features")));\r
}\r
\r
- this.addWindowListener(new WindowAdapter()\r
+ if (viewport.applet.getParameter("annotations") != null)\r
{\r
- public void windowClosing(WindowEvent e)\r
- {\r
- closeMenuItem_actionPerformed(null);\r
- }\r
- });\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("annotations")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("jnetfile") != null)\r
+ {\r
+ url.append("&annotations=");\r
+ url.append(appendProtocol(viewport.applet.getParameter("jnetfile")));\r
+ }\r
+\r
+ if (viewport.applet.getParameter("defaultColour") != null)\r
+ {\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(viewport.applet.getParameter("defaultColour"))\r
+ );\r
+ }\r
\r
- viewport.addPropertyChangeListener(new java.beans.PropertyChangeListener()\r
+ if (viewport.applet.getParameter("userDefinedColour") != null)\r
{\r
- public void propertyChange(java.beans.PropertyChangeEvent evt)\r
- {\r
- if (evt.getPropertyName().equals("alignment"))\r
- {\r
- alignmentChanged();\r
- }\r
- }\r
- });\r
+ url.append("&colour=" +\r
+ removeWhiteSpace(viewport.applet.getParameter(\r
+ "userDefinedColour"))\r
+ );\r
+ }\r
+\r
+ showURL(url.toString(), "FULL_APP");\r
}\r
\r
- public void inputText_actionPerformed(ActionEvent e)\r
+ String removeWhiteSpace(String colour)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(true, applet);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame, "Cut & Paste Input", 500, 500);\r
+ StringBuffer sb = new StringBuffer();\r
+ for (int i = 0; i < colour.length(); i++)\r
+ {\r
+ if (Character.isWhitespace(colour.charAt(i)))\r
+ {\r
+ sb.append("%20");\r
+ }\r
+ else\r
+ {\r
+ sb.append(colour.charAt(i));\r
+ }\r
+ }\r
+\r
+ return sb.toString();\r
}\r
\r
- protected void outputText_actionPerformed(ActionEvent e)\r
+ String appendProtocol(String url)\r
{\r
- CutAndPasteTransfer cap = new CutAndPasteTransfer(false, applet);\r
- Frame frame = new Frame();\r
- frame.add(cap);\r
- jalview.bin.JalviewLite.addFrame(frame,\r
- "Alignment output - " + e.getActionCommand(),\r
- 600, 500);\r
- cap.setText(FormatAdapter.formatSequences(e.getActionCommand(),\r
- viewport.getAlignment().\r
- getSequences()));\r
+ try\r
+ {\r
+ new URL(url);\r
+ }\r
+ catch (java.net.MalformedURLException ex)\r
+ {\r
+ url = viewport.applet.getCodeBase() + url;\r
+ }\r
+ return url;\r
}\r
\r
- public void closeMenuItem_actionPerformed(ActionEvent e)\r
+ public void closeMenuItem_actionPerformed()\r
{\r
- PaintRefresher.components.remove(viewport.alignment);\r
- dispose();\r
- if(PaintRefresher.components.size()==0 && applet==null)\r
+ PaintRefresher.RemoveComponent(alignPanel);\r
+ PaintRefresher.RemoveComponent(alignPanel.seqPanel.seqCanvas);\r
+ PaintRefresher.RemoveComponent(alignPanel.idPanel.idCanvas);\r
+\r
+ if (PaintRefresher.components.size() == 0 && viewport.applet == null)\r
+ {\r
System.exit(0);\r
- }\r
+ }\r
\r
- Stack historyList = new Stack();\r
- Stack redoList = new Stack();\r
+ this.dispose();\r
+ }\r
\r
+ /**\r
+ * DOCUMENT ME!\r
+ */\r
void updateEditMenuBar()\r
{\r
- if (historyList.size() > 0)\r
+\r
+ if (viewport.historyList.size() > 0)\r
{\r
undoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem) historyList.peek();\r
- undoMenuItem.setLabel("Undo " + hi.getDescription());\r
+ CommandI command = (CommandI) viewport.historyList.peek();\r
+ undoMenuItem.setLabel("Undo " + command.getDescription());\r
}\r
else\r
{\r
undoMenuItem.setLabel("Undo");\r
}\r
\r
- if (redoList.size() > 0)\r
+ if (viewport.redoList.size() > 0)\r
{\r
redoMenuItem.setEnabled(true);\r
- HistoryItem hi = (HistoryItem) redoList.peek();\r
- redoMenuItem.setLabel("Redo " + hi.getDescription());\r
+\r
+ CommandI command = (CommandI) viewport.redoList.peek();\r
+ redoMenuItem.setLabel("Redo " + command.getDescription());\r
}\r
else\r
{\r
}\r
}\r
\r
- public void addHistoryItem(HistoryItem hi)\r
+ public void addHistoryItem(CommandI command)\r
{\r
- historyList.push(hi);\r
- updateEditMenuBar();\r
+ if (command.getSize() > 0)\r
+ {\r
+ viewport.historyList.push(command);\r
+ viewport.redoList.removeAllElements();\r
+ updateEditMenuBar();\r
+ viewport.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+ }\r
}\r
\r
- protected void undoMenuItem_actionPerformed(ActionEvent e)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void undoMenuItem_actionPerformed()\r
{\r
- HistoryItem hi = (HistoryItem) historyList.pop();\r
- redoList.push(new HistoryItem(hi.getDescription(), viewport.alignment,\r
- HistoryItem.HIDE));\r
- restoreHistoryItem(hi);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
+ if (viewport.historyList.size() < 1)\r
+ {\r
+ return;\r
+ }\r
\r
- protected void redoMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- HistoryItem hi = (HistoryItem) redoList.pop();\r
- restoreHistoryItem(hi);\r
+ CommandI command = (CommandI) viewport.historyList.pop();\r
+ viewport.redoList.push(command);\r
+ command.undoCommand();\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
updateEditMenuBar();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ originalSource.firePropertyChange("alignment", null,\r
+ originalSource.alignment.getSequences());\r
}\r
\r
- // used by undo and redo\r
- void restoreHistoryItem(HistoryItem hi)\r
+ /**\r
+ * DOCUMENT ME!\r
+ *\r
+ * @param e DOCUMENT ME!\r
+ */\r
+ protected void redoMenuItem_actionPerformed()\r
{\r
- if (hi.getType() == HistoryItem.SORT)\r
+ if (viewport.redoList.size() < 1)\r
{\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
- {\r
- viewport.alignment.getSequences().setElementAt(hi.getSequences().\r
- elementAt(i), i);\r
- }\r
+ return;\r
}\r
- else\r
+\r
+ CommandI command = (CommandI) viewport.redoList.pop();\r
+ viewport.historyList.push(command);\r
+ command.doCommand();\r
+\r
+ AlignViewport originalSource = getOriginatingSource(command);\r
+ originalSource.hasHiddenColumns = viewport.colSel.getHiddenColumns() != null;\r
+\r
+ updateEditMenuBar();\r
+ originalSource.firePropertyChange("alignment", null,\r
+ originalSource.alignment.getSequences());\r
+ }\r
+\r
+ AlignViewport getOriginatingSource(CommandI command)\r
+ {\r
+ AlignViewport originalSource = null;\r
+ //For sequence removal and addition, we need to fire\r
+ //the property change event FROM the viewport where the\r
+ //original alignment was altered\r
+ AlignmentI al = null;\r
+ if (command instanceof EditCommand)\r
{\r
- for (int i = 0; i < hi.getSequences().size(); i++)\r
+ EditCommand editCommand = (EditCommand) command;\r
+ al = editCommand.getAlignment();\r
+ Vector comps = (Vector) PaintRefresher.components\r
+ .get(viewport.getSequenceSetId());\r
+ for (int i = 0; i < comps.size(); i++)\r
{\r
- SequenceI restore = (SequenceI) hi.getSequences().elementAt(i);\r
- if (restore.getLength() == 0)\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
{\r
- // log.System.out.println(hi.getHidden().elementAt(i));\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
- viewport.alignment.getSequences().insertElementAt(\r
- restore,\r
- hi.getAlignIndex(i));\r
- }\r
- else\r
- {\r
- restore.setSequence(hi.getHidden().elementAt(i).toString());\r
+ if (al == ( (AlignmentPanel) comps.elementAt(i)).av.alignment)\r
+ {\r
+ originalSource = ( (AlignmentPanel) comps.elementAt(i)).av;\r
+ break;\r
+ }\r
}\r
}\r
- if (hi.getType() == HistoryItem.PASTE)\r
+ }\r
+\r
+ if (originalSource == null)\r
+ {\r
+ //The original view is closed, we must validate\r
+ //the current view against the closed view first\r
+ if (al != null)\r
{\r
- for (int i = viewport.alignment.getHeight() - 1;\r
- i > hi.getSequences().size() - 1; i--)\r
- {\r
- viewport.alignment.deleteSequence(i);\r
- }\r
+ PaintRefresher.validateSequences(al, viewport.alignment);\r
}\r
- }\r
\r
- updateEditMenuBar();\r
+ originalSource = viewport;\r
+ }\r
\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ return originalSource;\r
}\r
\r
public void moveSelectedSequences(boolean up)\r
for (int i = 1; i < viewport.alignment.getHeight(); i++)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(null).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i - 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(null).contains(temp))\r
{\r
continue;\r
}\r
for (int i = viewport.alignment.getHeight() - 2; i > -1; i--)\r
{\r
SequenceI seq = viewport.alignment.getSequenceAt(i);\r
- if (!sg.sequences.contains(seq))\r
+ if (!sg.getSequences(viewport.hiddenRepSequences).contains(seq))\r
{\r
continue;\r
}\r
\r
SequenceI temp = viewport.alignment.getSequenceAt(i + 1);\r
- if (sg.sequences.contains(temp))\r
+ if (sg.getSequences(viewport.hiddenRepSequences).contains(temp))\r
{\r
continue;\r
}\r
}\r
}\r
\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
+ }\r
+\r
+ synchronized void slideSequences(boolean right, int size)\r
+ {\r
+ Vector sg = new Vector();\r
+ if(viewport.cursorMode)\r
+ {\r
+ sg.addElement(viewport.alignment.getSequenceAt(\r
+ alignPanel.seqPanel.seqCanvas.cursorY));\r
+ }\r
+ else if(viewport.getSelectionGroup()!=null\r
+ && viewport.getSelectionGroup().getSize()!=viewport.alignment.getHeight())\r
+ {\r
+ sg = viewport.getSelectionGroup().getSequences(\r
+ viewport.hiddenRepSequences);\r
+ }\r
+\r
+ if(sg.size()<1)\r
+ {\r
+ return;\r
+ }\r
+\r
+ Vector invertGroup = new Vector();\r
+\r
+ for (int i = 0; i < viewport.alignment.getHeight(); i++)\r
+ {\r
+ if(!sg.contains(viewport.alignment.getSequenceAt(i)))\r
+ invertGroup.addElement(viewport.alignment.getSequenceAt(i));\r
+ }\r
+\r
+ SequenceI[] seqs1 = new SequenceI[sg.size()];\r
+ for (int i = 0; i < sg.size(); i++)\r
+ seqs1[i] = (SequenceI) sg.elementAt(i);\r
+\r
+ SequenceI[] seqs2 = new SequenceI[invertGroup.size()];\r
+ for (int i = 0; i < invertGroup.size(); i++)\r
+ seqs2[i] = (SequenceI) invertGroup.elementAt(i);\r
+\r
+ SlideSequencesCommand ssc;\r
+ if (right)\r
+ ssc = new SlideSequencesCommand("Slide Sequences",\r
+ seqs2, seqs1, size,\r
+ viewport.getGapCharacter()\r
+ );\r
+ else\r
+ ssc = new SlideSequencesCommand("Slide Sequences",\r
+ seqs1, seqs2, size,\r
+ viewport.getGapCharacter()\r
+ );\r
+\r
+ int groupAdjustment = 0;\r
+ if (ssc.getGapsInsertedBegin() && right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor(size, 0);\r
+ else\r
+ groupAdjustment = size;\r
+ }\r
+ else if (!ssc.getGapsInsertedBegin() && !right)\r
+ {\r
+ if (viewport.cursorMode)\r
+ alignPanel.seqPanel.moveCursor( -size, 0);\r
+ else\r
+ groupAdjustment = -size;\r
+ }\r
+\r
+ if (groupAdjustment != 0)\r
+ {\r
+ viewport.getSelectionGroup().setStartRes(\r
+ viewport.getSelectionGroup().getStartRes() + groupAdjustment);\r
+ viewport.getSelectionGroup().setEndRes(\r
+ viewport.getSelectionGroup().getEndRes() + groupAdjustment);\r
+ }\r
+\r
+\r
+ boolean appendHistoryItem = false;\r
+ if(viewport.historyList!=null\r
+ && viewport.historyList.size()>0\r
+ && viewport.historyList.peek() instanceof SlideSequencesCommand)\r
+ {\r
+ appendHistoryItem = ssc.appendSlideCommand(\r
+ (SlideSequencesCommand)viewport.historyList.peek())\r
+ ;\r
+ }\r
+\r
+ if(!appendHistoryItem)\r
+ addHistoryItem(ssc);\r
+\r
+ repaint();\r
}\r
\r
- StringBuffer copiedSequences;\r
- protected void copy_actionPerformed(ActionEvent e)\r
+ static StringBuffer copiedSequences;\r
+ static Vector copiedHiddenColumns;\r
+ protected void copy_actionPerformed()\r
{\r
if (viewport.getSelectionGroup() == null)\r
{\r
int index = 0, startRes, endRes;\r
char ch;\r
\r
+ if (viewport.hasHiddenColumns && viewport.getSelectionGroup() != null)\r
+ {\r
+ copiedHiddenColumns = new Vector();\r
+ int hiddenOffset = viewport.getSelectionGroup().getStartRes();\r
+ for (int i = 0; i < viewport.getColumnSelection().getHiddenColumns().size();\r
+ i++)\r
+ {\r
+ int[] region = (int[])\r
+ viewport.getColumnSelection().getHiddenColumns().elementAt(i);\r
+\r
+ copiedHiddenColumns.addElement(new int[]\r
+ {region[0] - hiddenOffset,\r
+ region[1] - hiddenOffset});\r
+ }\r
+ }\r
+ else\r
+ {\r
+ copiedHiddenColumns = null;\r
+ }\r
+\r
for (int i = 0; i < sg.getSize(); i++)\r
{\r
- SequenceI seq = null;\r
+ SequenceI seq = null;\r
\r
- while (seq == null)\r
+ while (seq == null)\r
+ {\r
+ if (orderedSeqs.containsKey(index + ""))\r
{\r
- if (orderedSeqs.containsKey(index + ""))\r
- {\r
- seq = (SequenceI) orderedSeqs.get(index + "");\r
- index++;\r
+ seq = (SequenceI) orderedSeqs.get(index + "");\r
+ index++;\r
\r
- break;\r
- }\r
- else\r
- {\r
- index++;\r
- }\r
+ break;\r
}\r
+ else\r
+ {\r
+ index++;\r
+ }\r
+ }\r
\r
- //FIND START RES\r
- //Returns residue following index if gap\r
- startRes = seq.findPosition(sg.getStartRes());\r
+ //FIND START RES\r
+ //Returns residue following index if gap\r
+ startRes = seq.findPosition(sg.getStartRes());\r
\r
- //FIND END RES\r
- //Need to find the residue preceeding index if gap\r
- endRes = 0;\r
+ //FIND END RES\r
+ //Need to find the residue preceeding index if gap\r
+ endRes = 0;\r
\r
- for (int j = 0; j < sg.getEndRes()+1 && j < seq.getLength(); j++)\r
+ for (int j = 0; j < sg.getEndRes() + 1 && j < seq.getLength(); j++)\r
+ {\r
+ ch = seq.getCharAt(j);\r
+ if (!jalview.util.Comparison.isGap( (ch)))\r
{\r
- ch = seq.getCharAt(j);\r
- if (!jalview.util.Comparison.isGap( (ch)))\r
- {\r
- endRes++;\r
- }\r
+ endRes++;\r
}\r
+ }\r
\r
- if(endRes>0)\r
- {\r
- endRes += seq.getStart() -1;\r
- }\r
+ if (endRes > 0)\r
+ {\r
+ endRes += seq.getStart() - 1;\r
+ }\r
\r
- copiedSequences.append(seq.getName() + "\t" +\r
- startRes + "\t" +\r
- endRes + "\t" +\r
- seq.getSequence(sg.getStartRes(),\r
- sg.getEndRes() + 1) + "\n");\r
+ copiedSequences.append(seq.getName() + "\t" +\r
+ startRes + "\t" +\r
+ endRes + "\t" +\r
+ seq.getSequenceAsString(sg.getStartRes(),\r
+ sg.getEndRes() + 1) + "\n");\r
}\r
\r
}\r
\r
- protected void pasteNew_actionPerformed(ActionEvent e)\r
+ protected void pasteNew_actionPerformed()\r
{\r
paste(true);\r
}\r
\r
- protected void pasteThis_actionPerformed(ActionEvent e)\r
+ protected void pasteThis_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Paste Sequences", viewport.alignment,\r
- HistoryItem.PASTE));\r
paste(false);\r
}\r
\r
{\r
try\r
{\r
+\r
if (copiedSequences == null)\r
{\r
return;\r
String name = st.nextToken();\r
int start = Integer.parseInt(st.nextToken());\r
int end = Integer.parseInt(st.nextToken());\r
- Sequence sequence = new Sequence(name, st.nextToken(), start, end);\r
-\r
- if (!newAlignment)\r
- {\r
- viewport.alignment.addSequence(sequence);\r
- }\r
- else\r
- {\r
- seqs.addElement(sequence);\r
- }\r
+ seqs.addElement(new Sequence(name, st.nextToken(), start, end));\r
+ }\r
+ SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
}\r
\r
if (newAlignment)\r
{\r
- SequenceI[] newSeqs = new SequenceI[seqs.size()];\r
- for (int i = 0; i < seqs.size(); i++)\r
- {\r
- newSeqs[i] = (SequenceI) seqs.elementAt(i);\r
- }\r
-\r
- AlignFrame af = new AlignFrame(new Alignment(newSeqs), applet);\r
String newtitle = new String("Copied sequences");\r
if (getTitle().startsWith("Copied sequences"))\r
{\r
{\r
newtitle = newtitle.concat("- from " + getTitle());\r
}\r
- jalview.bin.JalviewLite.addFrame(af, newtitle, NEW_WINDOW_WIDTH,\r
- NEW_WINDOW_HEIGHT);\r
+ AlignFrame af = new AlignFrame(new Alignment(newSeqs),\r
+ viewport.applet,\r
+ newtitle,\r
+ false);\r
+ if (copiedHiddenColumns != null)\r
+ {\r
+ for (int i = 0; i < copiedHiddenColumns.size(); i++)\r
+ {\r
+ int[] region = (int[]) copiedHiddenColumns.elementAt(i);\r
+ af.viewport.hideColumns(region[0], region[1]);\r
+ }\r
+ }\r
+\r
+ jalview.bin.JalviewLite.addFrame(af, newtitle, DEFAULT_WIDTH,\r
+ DEFAULT_HEIGHT);\r
}\r
else\r
{\r
- viewport.setEndSeq(viewport.alignment.getHeight());\r
- viewport.alignment.getWidth();\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ addSequences(newSeqs);\r
}\r
\r
}\r
\r
}\r
\r
- protected void cut_actionPerformed(ActionEvent e)\r
+ void addSequences(SequenceI[] seqs)\r
{\r
- copy_actionPerformed(null);\r
- delete_actionPerformed(null);\r
+ for (int i = 0; i < seqs.length; i++)\r
+ {\r
+ viewport.alignment.addSequence(seqs[i]);\r
+ }\r
+\r
+ //!newAlignment\r
+ addHistoryItem(new EditCommand(\r
+ "Add sequences",\r
+ EditCommand.PASTE,\r
+ seqs,\r
+ 0,\r
+ viewport.alignment.getWidth(),\r
+ viewport.alignment)\r
+ );\r
+\r
+ viewport.setEndSeq(viewport.alignment.getHeight());\r
+ viewport.alignment.getWidth();\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.alignment.getSequences());\r
+\r
}\r
\r
- protected void delete_actionPerformed(ActionEvent e)\r
+ protected void cut_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Delete Sequences", viewport.alignment,\r
- HistoryItem.HIDE));\r
- if (viewport.getSelectionGroup() == null)\r
- {\r
- return;\r
- }\r
+ copy_actionPerformed();\r
+ delete_actionPerformed();\r
+ }\r
\r
+ protected void delete_actionPerformed()\r
+ {\r
\r
SequenceGroup sg = viewport.getSelectionGroup();\r
- boolean allSequences = false;\r
- if(sg.sequences.size()==viewport.alignment.getHeight())\r
- allSequences = true;\r
-\r
- for (int i = 0; i < sg.sequences.size(); i++)\r
+ if (sg == null)\r
{\r
- SequenceI seq = sg.getSequenceAt(i);\r
- int index = viewport.getAlignment().findIndex(seq);\r
- seq.deleteChars(sg.getStartRes(), sg.getEndRes() + 1);\r
+ return;\r
+ }\r
\r
- // If the cut affects all sequences, remove highlighted columns\r
- if (allSequences)\r
- {\r
- viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
- sg.getEndRes() + 1);\r
- }\r
+ Vector seqs = new Vector();\r
+ SequenceI seq;\r
+ for (int i = 0; i < sg.getSize(); i++)\r
+ {\r
+ seq = sg.getSequenceAt(i);\r
+ seqs.addElement(seq);\r
+ }\r
\r
+ // If the cut affects all sequences, remove highlighted columns\r
+ if (sg.getSize() == viewport.alignment.getHeight())\r
+ {\r
+ viewport.getColumnSelection().removeElements(sg.getStartRes(),\r
+ sg.getEndRes() + 1);\r
+ }\r
\r
- if (seq.getSequence().length() < 1)\r
- {\r
- viewport.getAlignment().deleteSequence(seq);\r
- }\r
- else\r
- {\r
- viewport.getAlignment().getSequences().setElementAt(seq, index);\r
- }\r
+ SequenceI[] cut = new SequenceI[seqs.size()];\r
+ for (int i = 0; i < seqs.size(); i++)\r
+ {\r
+ cut[i] = (SequenceI) seqs.elementAt(i);\r
}\r
\r
+ /*\r
+ //ADD HISTORY ITEM\r
+ */\r
+ addHistoryItem(new EditCommand("Cut Sequences",\r
+ EditCommand.CUT,\r
+ cut,\r
+ sg.getStartRes(),\r
+ sg.getEndRes() - sg.getStartRes() + 1,\r
+ viewport.alignment));\r
+\r
viewport.setSelectionGroup(null);\r
viewport.alignment.deleteGroup(sg);\r
- viewport.resetSeqLimits(alignPanel.seqPanel.seqCanvas.getSize().height);\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+\r
if (viewport.getAlignment().getHeight() < 1)\r
{\r
- try\r
- {\r
- this.setVisible(false);\r
- }\r
- catch (Exception ex)\r
- {}\r
+ this.setVisible(false);\r
}\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
-\r
}\r
\r
- protected void deleteGroups_actionPerformed(ActionEvent e)\r
+ protected void deleteGroups_actionPerformed()\r
{\r
viewport.alignment.deleteAllGroups();\r
+ viewport.sequenceColours = null;\r
viewport.setSelectionGroup(null);\r
\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
}\r
\r
- public void selectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void selectAllSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = new SequenceGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
sg.addSequence(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
- sg.setEndRes(viewport.alignment.getWidth()-1);\r
+ sg.setEndRes(viewport.alignment.getWidth() - 1);\r
viewport.setSelectionGroup(sg);\r
- alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void deselectAllSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void deselectAllSequenceMenuItem_actionPerformed()\r
{\r
+ if (viewport.cursorMode)\r
+ {\r
+ alignPanel.seqPanel.keyboardNo1 = null;\r
+ alignPanel.seqPanel.keyboardNo2 = null;\r
+ }\r
viewport.setSelectionGroup(null);\r
viewport.getColumnSelection().clear();\r
viewport.setSelectionGroup(null);\r
- alignPanel.repaint();\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
+ alignPanel.idPanel.idCanvas.searchResults = null;\r
+ alignPanel.seqPanel.seqCanvas.highlightSearchResults(null);\r
+ alignPanel.paintAlignment(true);\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void invertSequenceMenuItem_actionPerformed(ActionEvent e)\r
+ public void invertSequenceMenuItem_actionPerformed()\r
{\r
SequenceGroup sg = viewport.getSelectionGroup();\r
for (int i = 0; i < viewport.getAlignment().getSequences().size(); i++)\r
{\r
- sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
- }\r
-\r
- PaintRefresher.Refresh(null, viewport.alignment);\r
- }\r
-\r
- public void remove2LeftMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- ColumnSelection colSel = viewport.getColumnSelection();\r
- if (colSel.size() > 0)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Left", viewport.alignment,\r
- HistoryItem.HIDE));\r
- int min = colSel.getMin();\r
- viewport.getAlignment().trimLeft(min);\r
- colSel.compensateForEdit(0, min);\r
-\r
- if (viewport.getSelectionGroup() != null)\r
- {\r
- viewport.getSelectionGroup().adjustForRemoveLeft(min);\r
- }\r
-\r
- Vector groups = viewport.alignment.getGroups();\r
- for (int i = 0; i < groups.size(); i++)\r
- {\r
- SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (!sg.adjustForRemoveLeft(min))\r
- {\r
- viewport.alignment.deleteGroup(sg);\r
- }\r
- }\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
+ sg.addOrRemove(viewport.getAlignment().getSequenceAt(i), false);\r
}\r
+\r
+ PaintRefresher.Refresh(alignPanel, viewport.getSequenceSetId());\r
}\r
\r
- public void remove2RightMenuItem_actionPerformed(ActionEvent e)\r
+ void trimAlignment(boolean trimLeft)\r
{\r
ColumnSelection colSel = viewport.getColumnSelection();\r
+ int column;\r
+\r
if (colSel.size() > 0)\r
{\r
- addHistoryItem(new HistoryItem("Remove Right", viewport.alignment,\r
- HistoryItem.HIDE));\r
- int max = colSel.getMax();\r
- viewport.getAlignment().trimRight(max);\r
+ if (trimLeft)\r
+ {\r
+ column = colSel.getMin();\r
+ }\r
+ else\r
+ {\r
+ column = colSel.getMax();\r
+ }\r
+\r
+ SequenceI[] seqs;\r
if (viewport.getSelectionGroup() != null)\r
{\r
- viewport.getSelectionGroup().adjustForRemoveRight(max);\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
+ hiddenRepSequences);\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequencesArray();\r
+ }\r
+\r
+ TrimRegionCommand trimRegion;\r
+ if (trimLeft)\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Left",\r
+ TrimRegionCommand.TRIM_LEFT,\r
+ seqs,\r
+ column,\r
+ viewport.alignment,\r
+ viewport.colSel,\r
+ viewport.selectionGroup);\r
+ viewport.setStartRes(0);\r
+ }\r
+ else\r
+ {\r
+ trimRegion = new TrimRegionCommand("Remove Right",\r
+ TrimRegionCommand.TRIM_RIGHT,\r
+ seqs,\r
+ column,\r
+ viewport.alignment,\r
+ viewport.colSel,\r
+ viewport.selectionGroup);\r
}\r
\r
+ statusBar.setText("Removed " + trimRegion.getSize() + " columns.");\r
+\r
+ addHistoryItem(trimRegion);\r
+\r
Vector groups = viewport.alignment.getGroups();\r
+\r
for (int i = 0; i < groups.size(); i++)\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
- if (!sg.adjustForRemoveRight(max))\r
+\r
+ if ( (trimLeft && !sg.adjustForRemoveLeft(column))\r
+ || (!trimLeft && !sg.adjustForRemoveRight(column)))\r
{\r
viewport.alignment.deleteGroup(sg);\r
}\r
}\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
+ }\r
}\r
\r
- public void removeGappedColumnMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeGappedColumnMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Remove Gapped Columns",\r
- viewport.alignment,\r
- HistoryItem.HIDE));\r
+ int start = 0, end = viewport.alignment.getWidth() - 1;\r
\r
- //This is to maintain viewport position on first residue\r
- //of first sequence\r
- SequenceI seq = viewport.alignment.getSequenceAt(0);\r
- int startRes = seq.findPosition(viewport.startRes);\r
-\r
- viewport.getAlignment().removeGaps();\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
+ {\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
+ hiddenRepSequences);\r
+ start = viewport.getSelectionGroup().getStartRes();\r
+ end = viewport.getSelectionGroup().getEndRes();\r
+ }\r
+ else\r
+ {\r
+ seqs = viewport.alignment.getSequencesArray();\r
+ }\r
\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
+ RemoveGapColCommand removeGapCols =\r
+ new RemoveGapColCommand("Remove Gapped Columns",\r
+ seqs,\r
+ start, end,\r
+ viewport.alignment);\r
\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
- }\r
+ addHistoryItem(removeGapCols);\r
\r
- public void removeAllGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- addHistoryItem(new HistoryItem("Remove Gaps", viewport.alignment,\r
- HistoryItem.HIDE));\r
+ statusBar.setText("Removed " + removeGapCols.getSize() + " empty columns.");\r
\r
//This is to maintain viewport position on first residue\r
//of first sequence\r
SequenceI seq = viewport.alignment.getSequenceAt(0);\r
int startRes = seq.findPosition(viewport.startRes);\r
+ // ShiftList shifts;\r
+ // viewport.getAlignment().removeGaps(shifts=new ShiftList());\r
+ // edit.alColumnChanges=shifts.getInverse();\r
+ // if (viewport.hasHiddenColumns)\r
+ // viewport.getColumnSelection().compensateForEdits(shifts);\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
\r
- SequenceI current;\r
- int jSize;\r
-\r
- Vector seqs=null;\r
+ }\r
\r
- int start=0, end = viewport.alignment.getWidth();\r
+ public void removeAllGapsMenuItem_actionPerformed()\r
+ {\r
+ int start = 0, end = viewport.alignment.getWidth() - 1;\r
\r
- if (viewport.getSelectionGroup() != null\r
- && viewport.getSelectionGroup().sequences != null\r
- && viewport.getSelectionGroup().sequences.size()>0)\r
+ SequenceI[] seqs;\r
+ if (viewport.getSelectionGroup() != null)\r
{\r
- seqs = viewport.getSelectionGroup().sequences;\r
+ seqs = viewport.getSelectionGroup().getSequencesAsArray(viewport.\r
+ hiddenRepSequences);\r
start = viewport.getSelectionGroup().getStartRes();\r
- end = viewport.getSelectionGroup().getEndRes()+1;\r
+ end = viewport.getSelectionGroup().getEndRes();\r
}\r
else\r
- seqs = viewport.alignment.getSequences();\r
-\r
- for (int i = 0; i < seqs.size(); i++)\r
{\r
- current = (SequenceI) seqs.elementAt(i);\r
- jSize = current.getLength();\r
+ seqs = viewport.alignment.getSequencesArray();\r
+ }\r
+\r
+ //This is to maintain viewport position on first residue\r
+ //of first sequence\r
+ SequenceI seq = viewport.alignment.getSequenceAt(0);\r
+ int startRes = seq.findPosition(viewport.startRes);\r
\r
- // Removing a range is much quicker than removing gaps\r
- // one by one for long sequences\r
- int j = start;\r
- int rangeStart=-1, rangeEnd=-1;\r
+ addHistoryItem(new RemoveGapsCommand("Remove Gaps",\r
+ seqs,\r
+ start, end,\r
+ viewport.alignment));\r
+\r
+ viewport.setStartRes(seq.findIndex(startRes) - 1);\r
+\r
+ viewport.firePropertyChange("alignment", null,\r
+ viewport.getAlignment().getSequences());\r
\r
- do\r
- {\r
- if (jalview.util.Comparison.isGap(current.getCharAt(j)))\r
- {\r
- if(rangeStart==-1)\r
- {\r
- rangeStart = j;\r
- rangeEnd = j+1;\r
- }\r
- else\r
- {\r
- rangeEnd++;\r
- }\r
- j++;\r
- }\r
- else\r
- {\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- j-=rangeEnd-rangeStart;\r
- jSize-=rangeEnd-rangeStart;\r
- rangeStart = -1;\r
- rangeEnd = -1;\r
- }\r
- else\r
- j++;\r
- }\r
- }\r
- while (j < end && j < jSize);\r
- if(rangeStart>-1)\r
- {\r
- current.deleteChars(rangeStart, rangeEnd);\r
- }\r
- }\r
- viewport.setStartRes(seq.findIndex(startRes)-1);\r
- viewport.firePropertyChange("alignment", null, viewport.getAlignment().getSequences());\r
}\r
\r
- public void alignmentChanged()\r
+ public void findMenuItem_actionPerformed()\r
{\r
- viewport.updateConsensus();\r
- viewport.updateConservation ();\r
- resetAllColourSchemes();\r
- if(alignPanel.overviewPanel!=null)\r
- alignPanel.overviewPanel.updateOverviewImage();\r
- alignPanel.repaint();\r
+ new Finder(alignPanel);\r
}\r
\r
- void resetAllColourSchemes()\r
+ public void newView()\r
{\r
- ColourSchemeI cs = viewport.globalColourScheme;\r
- if(cs!=null)\r
+ AlignmentI newal;\r
+ if (viewport.hasHiddenRows)\r
{\r
- if (cs instanceof ClustalxColourScheme)\r
- {\r
- ( (ClustalxColourScheme) viewport.getGlobalColourScheme()).\r
- resetClustalX(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth());\r
- }\r
+ newal = new Alignment(viewport.getAlignment().\r
+ getHiddenSequences()\r
+ .getFullAlignment().\r
+ getSequencesArray());\r
+ }\r
+ else\r
+ {\r
+ newal = new Alignment(viewport.alignment.getSequencesArray());\r
+ }\r
\r
- cs.setConsensus(viewport.vconsensus);\r
- if (cs.conservationApplied())\r
+ if (viewport.alignment.getAlignmentAnnotation() != null)\r
+ {\r
+ for (int i = 0; i < viewport.alignment.getAlignmentAnnotation().length; i++)\r
{\r
- Alignment al = (Alignment) viewport.alignment;\r
- Conservation c = new Conservation("All",\r
- ResidueProperties.propHash, 3,\r
- al.getSequences(), 0,\r
- al.getWidth() - 1);\r
- c.calculate();\r
- c.verdict(false, viewport.ConsPercGaps);\r
-\r
- cs.setConservation(c);\r
+ if (!viewport.alignment.getAlignmentAnnotation()[i].autoCalculated)\r
+ {\r
+ newal.addAnnotation(viewport.alignment.getAlignmentAnnotation()[i]);\r
+ }\r
}\r
}\r
\r
- int s, sSize = viewport.alignment.getGroups().size();\r
- for(s=0; s<sSize; s++)\r
+ AlignFrame newaf = new AlignFrame(newal,\r
+ viewport.applet,\r
+ "",\r
+ false);\r
+\r
+ newaf.viewport.sequenceSetID = alignPanel.av.getSequenceSetId();\r
+ PaintRefresher.Register(alignPanel, alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ PaintRefresher.Register(newaf.alignPanel.idPanel.idCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+ PaintRefresher.Register(newaf.alignPanel.seqPanel.seqCanvas,\r
+ newaf.alignPanel.av.getSequenceSetId());\r
+\r
+ Vector comps = (Vector) PaintRefresher.components.get(viewport.\r
+ getSequenceSetId());\r
+ int viewSize = -1;\r
+ for (int i = 0; i < comps.size(); i++)\r
{\r
- SequenceGroup sg = (SequenceGroup)viewport.alignment.getGroups().elementAt(s);\r
- if(sg.cs!=null && sg.cs instanceof ClustalxColourScheme)\r
+ if (comps.elementAt(i) instanceof AlignmentPanel)\r
{\r
- ((ClustalxColourScheme)sg.cs).resetClustalX(sg.sequences, sg.getWidth());\r
+ viewSize++;\r
}\r
- sg.recalcConservation();\r
}\r
- }\r
\r
+ String title = new String(this.getTitle());\r
+ if (title.indexOf("(View") > -1)\r
+ {\r
+ title = title.substring(0, title.indexOf("(View"));\r
+ }\r
\r
+ title += "(View " + viewSize + ")";\r
\r
- public void findMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- Finder finder = new Finder(alignPanel);\r
- }\r
+ newaf.setTitle(title.toString());\r
\r
- public void font_actionPerformed(ActionEvent e)\r
- {\r
- Frame frame = new Frame();\r
- FontChooser fc = new FontChooser(alignPanel, frame);\r
- frame.add(fc);\r
- jalview.bin.JalviewLite.addFrame(frame, "Change Font", 440, 100);\r
+ newaf.viewport.historyList = viewport.historyList;\r
+ newaf.viewport.redoList = viewport.redoList;\r
\r
}\r
\r
- protected void fullSeqId_actionPerformed(ActionEvent e)\r
+ public void seqLimits_itemStateChanged()\r
{\r
- viewport.setShowFullId(fullSeqId.getState());\r
+ viewport.setShowJVSuffix(seqLimits.getState());\r
alignPanel.fontChanged();\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
}\r
\r
- protected void colourTextMenuItem_actionPerformed(ActionEvent e)\r
+ protected void colourTextMenuItem_actionPerformed()\r
{\r
viewport.setColourText(colourTextMenuItem.getState());\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
}\r
\r
- protected void wrapMenuItem_actionPerformed(ActionEvent e)\r
+ protected void wrapMenuItem_actionPerformed()\r
{\r
viewport.setWrapAlignment(wrapMenuItem.getState());\r
alignPanel.setWrapAlignment(wrapMenuItem.getState());\r
scaleAbove.setEnabled(wrapMenuItem.getState());\r
scaleLeft.setEnabled(wrapMenuItem.getState());\r
scaleRight.setEnabled(wrapMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleAbove_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleAboveWrapped(scaleAbove.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleLeft_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleLeftWrapped(scaleLeft.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void scaleRight_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setScaleRightWrapped(scaleRight.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewBoxesMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowBoxes(viewBoxesMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void viewTextMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setShowText(viewTextMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- protected void renderGapsMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setRenderGaps(renderGapsMenuItem.getState());\r
- alignPanel.repaint();\r
- }\r
-\r
- public void annotationPanelMenuItem_actionPerformed(ActionEvent e)\r
- {\r
- if (annotationPanelMenuItem.getState() && viewport.getWrapAlignment())\r
- {\r
- annotationPanelMenuItem.setState(false);\r
- return;\r
- }\r
- viewport.setShowAnnotation(annotationPanelMenuItem.getState());\r
- alignPanel.setAnnotationVisible(annotationPanelMenuItem.getState());\r
+ alignPanel.paintAlignment(true);\r
}\r
\r
- public void overviewMenuItem_actionPerformed(ActionEvent e)\r
+ public void overviewMenuItem_actionPerformed()\r
{\r
if (alignPanel.overviewPanel != null)\r
{\r
frame.add(overview);\r
// +50 must allow for applet frame window\r
jalview.bin.JalviewLite.addFrame(frame, "Overview " + this.getTitle(),\r
- overview.preferredSize().width,\r
- overview.preferredSize().height + 50);\r
+ overview.getPreferredSize().width,\r
+ overview.getPreferredSize().height + 50);\r
\r
frame.pack();\r
frame.addWindowListener(new WindowAdapter()\r
\r
}\r
\r
- protected void noColourmenuItem_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(null);\r
- }\r
-\r
- public void clustalColour_actionPerformed(ActionEvent e)\r
- {\r
- abovePIDThreshold.setState(false);\r
- changeColour(new ClustalxColourScheme(viewport.alignment.getSequences(),\r
- viewport.alignment.getWidth()));\r
- }\r
-\r
- public void zappoColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new ZappoColourScheme());\r
- }\r
-\r
- public void taylorColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TaylorColourScheme());\r
- }\r
-\r
- public void hydrophobicityColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HydrophobicColourScheme());\r
- }\r
-\r
- public void helixColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new HelixColourScheme());\r
- }\r
-\r
- public void strandColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new StrandColourScheme());\r
- }\r
-\r
- public void turnColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new TurnColourScheme());\r
- }\r
-\r
- public void buriedColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new BuriedColourScheme());\r
- }\r
-\r
- public void nucleotideColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new NucleotideColourScheme());\r
- }\r
-\r
- protected void applyToAllGroups_actionPerformed(ActionEvent e)\r
- {\r
- viewport.setColourAppliesToAllGroups(applyToAllGroups.getState());\r
- }\r
-\r
void changeColour(ColourSchemeI cs)\r
{\r
int threshold = 0;\r
\r
- if(cs!=null)\r
+ if (cs != null)\r
{\r
if (viewport.getAbovePIDThreshold())\r
{\r
cs.setConservation(null);\r
}\r
\r
- cs.setConsensus(viewport.vconsensus);\r
+ cs.setConsensus(viewport.hconsensus);\r
\r
}\r
viewport.setGlobalColourScheme(cs);\r
{\r
SequenceGroup sg = (SequenceGroup) groups.elementAt(i);\r
\r
- if(cs==null)\r
+ if (cs == null)\r
{\r
sg.cs = null;\r
continue;\r
}\r
if (cs instanceof ClustalxColourScheme)\r
{\r
- sg.cs = new ClustalxColourScheme(sg.sequences, sg.getWidth());\r
+ sg.cs = new ClustalxColourScheme(\r
+ sg.getSequences(viewport.hiddenRepSequences),\r
+ sg.getWidth());\r
}\r
else\r
{\r
|| cs instanceof Blosum62ColourScheme)\r
{\r
sg.cs.setThreshold(threshold, viewport.getIgnoreGapsConsensus());\r
- sg.cs.setConsensus(AAFrequency.calculate(sg.sequences, 0, sg.getWidth()));\r
+ sg.cs.setConsensus(AAFrequency.calculate(\r
+ sg.getSequences(viewport.hiddenRepSequences), 0, sg.getWidth()));\r
}\r
else\r
+ {\r
sg.cs.setThreshold(0, viewport.getIgnoreGapsConsensus());\r
+ }\r
\r
if (viewport.getConservationSelected())\r
{\r
Conservation c = new Conservation("Group",\r
ResidueProperties.propHash, 3,\r
- sg.sequences, 0,\r
+ sg.getSequences(viewport.\r
+ hiddenRepSequences), 0,\r
viewport.alignment.getWidth() - 1);\r
c.calculate();\r
c.verdict(false, viewport.ConsPercGaps);\r
}\r
}\r
\r
-\r
if (alignPanel.getOverviewPanel() != null)\r
{\r
alignPanel.getOverviewPanel().updateOverviewImage();\r
}\r
\r
- alignPanel.repaint();\r
- }\r
-\r
+ jalview.structure.StructureSelectionManager.getStructureSelectionManager()\r
+ .sequenceColoursChanged(alignPanel);\r
\r
+ alignPanel.paintAlignment(true);\r
+ }\r
\r
- protected void modifyPID_actionPerformed(ActionEvent e)\r
+ protected void modifyPID_actionPerformed()\r
{\r
- if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme!=null)\r
+ if (viewport.getAbovePIDThreshold() && viewport.globalColourScheme != null)\r
{\r
SliderPanel.setPIDSliderSource(alignPanel, viewport.getGlobalColourScheme(),\r
"Background");\r
}\r
}\r
\r
- protected void modifyConservation_actionPerformed(ActionEvent e)\r
+ protected void modifyConservation_actionPerformed()\r
{\r
- if (viewport.getConservationSelected() && viewport.globalColourScheme!=null)\r
+ if (viewport.getConservationSelected() && viewport.globalColourScheme != null)\r
{\r
SliderPanel.setConservationSlider(alignPanel, viewport.globalColourScheme,\r
"Background");\r
}\r
}\r
\r
- protected void conservationMenuItem_actionPerformed(ActionEvent e)\r
+ protected void conservationMenuItem_actionPerformed()\r
{\r
viewport.setConservationSelected(conservationMenuItem.getState());\r
\r
\r
changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyConservation_actionPerformed(null);\r
+ modifyConservation_actionPerformed();\r
}\r
\r
- public void abovePIDThreshold_actionPerformed(ActionEvent e)\r
+ public void abovePIDThreshold_actionPerformed()\r
{\r
viewport.setAbovePIDThreshold(abovePIDThreshold.getState());\r
\r
\r
changeColour(viewport.getGlobalColourScheme());\r
\r
- modifyPID_actionPerformed(null);\r
- }\r
-\r
- public void userDefinedColour_actionPerformed(ActionEvent e)\r
- {\r
- UserDefinedColours chooser = new UserDefinedColours(alignPanel, null);\r
- }\r
-\r
- public void PIDColour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new PIDColourScheme());\r
- }\r
-\r
- public void BLOSUM62Colour_actionPerformed(ActionEvent e)\r
- {\r
- changeColour(new Blosum62ColourScheme());\r
+ modifyPID_actionPerformed();\r
}\r
\r
- public void sortPairwiseMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortPairwiseMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Pairwise Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ SequenceI[] oldOrder = viewport.getAlignment().getSequencesArray();\r
AlignmentSorter.sortByPID(viewport.getAlignment(),\r
viewport.getAlignment().getSequenceAt(0));\r
- alignPanel.repaint();\r
+ addHistoryItem(new OrderCommand("Pairwise Sort", oldOrder,\r
+ viewport.alignment));\r
+ alignPanel.paintAlignment(true);\r
}\r
\r
- public void sortIDMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortIDMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // addHistoryItem(new HistoryItem("ID Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByID(viewport.getAlignment());\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
}\r
\r
- public void sortGroupMenuItem_actionPerformed(ActionEvent e)\r
+ public void sortGroupMenuItem_actionPerformed()\r
{\r
- addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // addHistoryItem(new HistoryItem("Group Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByGroup(viewport.getAlignment());\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
\r
}\r
\r
- public void removeRedundancyMenuItem_actionPerformed(ActionEvent e)\r
+ public void removeRedundancyMenuItem_actionPerformed()\r
{\r
- RedundancyPanel sp = new RedundancyPanel(alignPanel);\r
- Frame frame = new Frame();\r
- frame.add(sp);\r
- jalview.bin.JalviewLite.addFrame(frame, "Redundancy threshold selection",\r
- 400, 120);\r
-\r
+ new RedundancyPanel(alignPanel);\r
}\r
\r
- public void pairwiseAlignmentMenuItem_actionPerformed(ActionEvent e)\r
+ public void pairwiseAlignmentMenuItem_actionPerformed()\r
{\r
- if (viewport.getSelectionGroup().getSize() > 1)\r
+ if (viewport.getSelectionGroup() != null\r
+ && viewport.getSelectionGroup().getSize() > 1)\r
{\r
Frame frame = new Frame();\r
frame.add(new PairwiseAlignPanel(alignPanel));\r
}\r
}\r
\r
- public void PCAMenuItem_actionPerformed(ActionEvent e)\r
+ public void PCAMenuItem_actionPerformed()\r
{\r
+ //are the sequences aligned?\r
+ if (!viewport.alignment.isAligned())\r
+ {\r
+ SequenceI current;\r
+ int Width = viewport.getAlignment().getWidth();\r
+\r
+ for (int i = 0; i < viewport.getAlignment().getSequences().size();\r
+ i++)\r
+ {\r
+ current = viewport.getAlignment().getSequenceAt(i);\r
+\r
+ if (current.getLength() < Width)\r
+ {\r
+ current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
+ }\r
+ }\r
+ alignPanel.paintAlignment(true);\r
+ }\r
\r
if ( (viewport.getSelectionGroup() != null &&\r
viewport.getSelectionGroup().getSize() < 4 &&\r
\r
try\r
{\r
- PCAPanel pcaPanel = new PCAPanel(viewport);\r
- Frame frame = new Frame();\r
- frame.add(pcaPanel);\r
- jalview.bin.JalviewLite.addFrame(frame, "Principal component analysis",\r
- 400, 400);\r
+ new PCAPanel(viewport);\r
}\r
catch (java.lang.OutOfMemoryError ex)\r
{\r
\r
}\r
\r
- public void averageDistanceTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void averageDistanceTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("AV", "PID", "Average distance tree using PID");\r
}\r
\r
- public void neighbourTreeMenuItem_actionPerformed(ActionEvent e)\r
+ public void neighbourTreeMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "PID", "Neighbour joining tree using PID");\r
}\r
\r
- protected void njTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void njTreeBlosumMenuItem_actionPerformed()\r
{\r
NewTreePanel("NJ", "BL", "Neighbour joining tree using BLOSUM62");\r
}\r
\r
- protected void avTreeBlosumMenuItem_actionPerformed(ActionEvent e)\r
+ protected void avTreeBlosumMenuItem_actionPerformed()\r
{\r
- NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62PID");\r
+ NewTreePanel("AV", "BL", "Average distance tree using BLOSUM62");\r
}\r
\r
void NewTreePanel(String type, String pwType, String title)\r
current.insertCharAt(Width - 1, viewport.getGapCharacter());\r
}\r
}\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
\r
}\r
\r
- final TreePanel tp;\r
- if (viewport.getSelectionGroup() != null &&\r
- viewport.getSelectionGroup().getSize() > 3)\r
- {\r
- tp = new TreePanel(viewport, viewport.getSelectionGroup().sequences, type,\r
- pwType,\r
- 0, viewport.alignment.getWidth());\r
- }\r
- else\r
+ if ( (viewport.getSelectionGroup() != null &&\r
+ viewport.getSelectionGroup().getSize() > 1)\r
+ || (viewport.getSelectionGroup() == null\r
+ && viewport.alignment.getHeight() > 1))\r
{\r
- tp = new TreePanel(viewport, viewport.getAlignment().getSequences(),\r
- type, pwType, 0, viewport.alignment.getWidth());\r
+ final TreePanel tp = new TreePanel(viewport,\r
+ type,\r
+ pwType);\r
+\r
+ addTreeMenuItem(tp, title);\r
+\r
+ jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
}\r
+ }\r
\r
- addTreeMenuItem(tp, title);\r
+ void loadTree_actionPerformed()\r
+ {\r
+ CutAndPasteTransfer cap = new CutAndPasteTransfer(true, this);\r
+ cap.setText("Paste your Newick tree file here.");\r
+ cap.setTreeImport();\r
+ Frame frame = new Frame();\r
+ frame.add(cap);\r
+ jalview.bin.JalviewLite.addFrame(frame, "Paste Newick file ", 400, 300);\r
+ }\r
\r
- jalview.bin.JalviewLite.addFrame(tp, title, 600, 500);\r
+ public void loadTree(jalview.io.NewickFile tree, String treeFile)\r
+ {\r
+ TreePanel tp = new TreePanel(viewport,\r
+ treeFile,\r
+ "From File - ",\r
+ tree);\r
+ jalview.bin.JalviewLite.addFrame(tp, treeFile, 600, 500);\r
+ addTreeMenuItem(tp, treeFile);\r
}\r
\r
void addTreeMenuItem(final TreePanel treePanel, String title)\r
sortByTreeMenu.add(item);\r
item.addActionListener(new java.awt.event.ActionListener()\r
{\r
- public void actionPerformed(ActionEvent e)\r
+ public void actionPerformed(ActionEvent evt)\r
{\r
- addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
- HistoryItem.SORT));\r
+ // addHistoryItem(new HistoryItem("Sort", viewport.alignment,\r
+ // HistoryItem.SORT));\r
AlignmentSorter.sortByTree(viewport.getAlignment(), treePanel.getTree());\r
- alignPanel.repaint();\r
+ alignPanel.paintAlignment(true);\r
}\r
});\r
\r
});\r
}\r
\r
- protected void documentation_actionPerformed(ActionEvent e)\r
+ protected void documentation_actionPerformed()\r
{\r
- jalview.bin.JalviewLite.showURL("http://www.jalview.org/help.html");\r
+ showURL("http://www.jalview.org/help.html", "HELP");\r
}\r
\r
- protected void about_actionPerformed(ActionEvent e)\r
+ protected void about_actionPerformed()\r
{\r
\r
- class AboutPanel extends Canvas\r
+ class AboutPanel\r
+ extends Canvas\r
{\r
String version;\r
public AboutPanel(String version)\r
- { this.version = version; }\r
+ {\r
+ this.version = version;\r
+ }\r
\r
public void paint(Graphics g)\r
{\r
int y = 5, x = 7;\r
g.setColor(Color.black);\r
g.setFont(new Font("Helvetica", Font.BOLD, 14));\r
- g.drawString("Jalview - Release "+version, 200, y += fh);\r
+ g.drawString("Jalview - Release " + version, 200, y += fh);\r
g.setFont(new Font("Helvetica", Font.PLAIN, 12));\r
g.drawString("Authors: Michele Clamp, James Cuff, Steve Searle, Andrew Waterhouse, Jim Procter & Geoff Barton.",\r
x, y += fh * 2);\r
g.drawString("If you use JalView, please cite:", x, y += fh + 8);\r
g.drawString("\"Clamp, M., Cuff, J., Searle, S. M. and Barton, G. J. (2004), The Jalview Java Alignment Editor\"",\r
x, y += fh);\r
- g.drawString("Bioinformatics, 2004 12;426-7.", x, y += fh);\r
+ g.drawString("Bioinformatics, 2004 20;426-7.", x, y += fh);\r
}\r
}\r
\r
}\r
}\r
\r
-\r
Frame frame = new Frame();\r
frame.add(new AboutPanel(version));\r
jalview.bin.JalviewLite.addFrame(frame, "Jalview", 580, 200);\r
\r
}\r
+\r
+ public void showURL(String url, String target)\r
+ {\r
+ if (viewport.applet == null)\r
+ {\r
+ System.out.println("Not running as applet - no browser available.");\r
+ }\r
+ else\r
+ {\r
+ try\r
+ {\r
+ System.out.println("Show url: " + url);\r
+ viewport.applet.getAppletContext().showDocument(new java.net.URL(url),\r
+ target);\r
+ }\r
+ catch (Exception ex)\r
+ {\r
+ ex.printStackTrace();\r
+ }\r
+ }\r
+ }\r
+\r
+ //////////////////////////////////////////////////////////////////////////////////\r
+ //JBuilder Graphics here\r
+\r
+ protected MenuBar alignFrameMenuBar = new MenuBar();\r
+ protected Menu fileMenu = new Menu("File");\r
+ protected MenuItem loadApplication = new MenuItem("View in Full Application");\r
+ protected MenuItem loadTree = new MenuItem("Load Associated Tree ...");\r
+ protected MenuItem loadAnnotations = new MenuItem(\r
+ "Load Features/Annotations ...");\r
+ protected MenuItem outputFeatures = new MenuItem("Export Features ...");\r
+ protected MenuItem outputAnnotations = new MenuItem("Export Annotations ...");\r
+\r
+ protected MenuItem closeMenuItem = new MenuItem("Close");\r
+ protected Menu editMenu = new Menu("Edit");\r
+ protected Menu viewMenu = new Menu("View");\r
+ protected Menu colourMenu = new Menu("Colour");\r
+ protected Menu calculateMenu = new Menu("Calculate");\r
+ protected MenuItem selectAllSequenceMenuItem = new MenuItem("Select all");\r
+ protected MenuItem deselectAllSequenceMenuItem = new MenuItem("Deselect All");\r
+ protected MenuItem invertSequenceMenuItem = new MenuItem("Invert Selection");\r
+ protected MenuItem remove2LeftMenuItem = new MenuItem();\r
+ protected MenuItem remove2RightMenuItem = new MenuItem();\r
+ protected MenuItem removeGappedColumnMenuItem = new MenuItem();\r
+ protected MenuItem removeAllGapsMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem viewBoxesMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem viewTextMenuItem = new CheckboxMenuItem();\r
+ protected MenuItem sortPairwiseMenuItem = new MenuItem();\r
+ protected MenuItem sortIDMenuItem = new MenuItem();\r
+ protected MenuItem sortGroupMenuItem = new MenuItem();\r
+ protected MenuItem removeRedundancyMenuItem = new MenuItem();\r
+ protected MenuItem pairwiseAlignmentMenuItem = new MenuItem();\r
+ protected MenuItem PCAMenuItem = new MenuItem();\r
+ protected MenuItem averageDistanceTreeMenuItem = new MenuItem();\r
+ protected MenuItem neighbourTreeMenuItem = new MenuItem();\r
+ BorderLayout borderLayout1 = new BorderLayout();\r
+ public Label statusBar = new Label();\r
+ protected Menu outputTextboxMenu = new Menu();\r
+ protected MenuItem clustalColour = new MenuItem();\r
+ protected MenuItem zappoColour = new MenuItem();\r
+ protected MenuItem taylorColour = new MenuItem();\r
+ protected MenuItem hydrophobicityColour = new MenuItem();\r
+ protected MenuItem helixColour = new MenuItem();\r
+ protected MenuItem strandColour = new MenuItem();\r
+ protected MenuItem turnColour = new MenuItem();\r
+ protected MenuItem buriedColour = new MenuItem();\r
+ protected MenuItem userDefinedColour = new MenuItem();\r
+ protected MenuItem PIDColour = new MenuItem();\r
+ protected MenuItem BLOSUM62Colour = new MenuItem();\r
+ MenuItem njTreeBlosumMenuItem = new MenuItem();\r
+ MenuItem avDistanceTreeBlosumMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem annotationPanelMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem colourTextMenuItem = new CheckboxMenuItem();\r
+ MenuItem overviewMenuItem = new MenuItem();\r
+ protected MenuItem undoMenuItem = new MenuItem();\r
+ protected MenuItem redoMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem conservationMenuItem = new CheckboxMenuItem();\r
+ MenuItem noColourmenuItem = new MenuItem();\r
+ protected CheckboxMenuItem wrapMenuItem = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem renderGapsMenuItem = new CheckboxMenuItem();\r
+ MenuItem findMenuItem = new MenuItem();\r
+ protected CheckboxMenuItem abovePIDThreshold = new CheckboxMenuItem();\r
+ protected MenuItem nucleotideColour = new MenuItem();\r
+ MenuItem deleteGroups = new MenuItem();\r
+ MenuItem delete = new MenuItem();\r
+ MenuItem copy = new MenuItem();\r
+ MenuItem cut = new MenuItem();\r
+ Menu pasteMenu = new Menu();\r
+ MenuItem pasteNew = new MenuItem();\r
+ MenuItem pasteThis = new MenuItem();\r
+ protected CheckboxMenuItem applyToAllGroups = new CheckboxMenuItem();\r
+ protected MenuItem font = new MenuItem();\r
+ protected CheckboxMenuItem scaleAbove = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleLeft = new CheckboxMenuItem();\r
+ protected CheckboxMenuItem scaleRight = new CheckboxMenuItem();\r
+ MenuItem modifyPID = new MenuItem();\r
+ MenuItem modifyConservation = new MenuItem();\r
+ protected CheckboxMenuItem autoCalculate\r
+ = new CheckboxMenuItem("Autocalculate Consensus", true);\r
+ protected Menu sortByTreeMenu = new Menu();\r
+ Menu sort = new Menu();\r
+ Menu calculate = new Menu();\r
+ MenuItem inputText = new MenuItem();\r
+ Menu helpMenu = new Menu();\r
+ MenuItem documentation = new MenuItem();\r
+ MenuItem about = new MenuItem();\r
+ protected CheckboxMenuItem seqLimits = new CheckboxMenuItem();\r
+ Panel embeddedMenu;\r
+ Label embeddedEdit;\r
+ Label embeddedSelect;\r
+ Label embeddedView;\r
+ Label embeddedFormat;\r
+ Label embeddedColour;\r
+ Label embeddedFile;\r
+ Label embeddedHelp;\r
+ Label embeddedCalculate;\r
+ FlowLayout flowLayout1;\r
+\r
+ private void jbInit()\r
+ throws Exception\r
+ {\r
+\r
+ setMenuBar(alignFrameMenuBar);\r
+\r
+ MenuItem item;\r
+\r
+ // dynamically fill save as menu with available formats\r
+ for (int i = 0; i < jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS.length;\r
+ i++)\r
+ {\r
+\r
+ item = new MenuItem(jalview.io.AppletFormatAdapter.WRITEABLE_FORMATS[i]);\r
+\r
+ item.addActionListener(new java.awt.event.ActionListener()\r
+ {\r
+ public void actionPerformed(ActionEvent e)\r
+ {\r
+ outputText_actionPerformed(e);\r
+ }\r
+ });\r
+\r
+ outputTextboxMenu.add(item);\r
+ }\r
+ closeMenuItem.addActionListener(this);\r
+ loadApplication.addActionListener(this);\r
+\r
+ loadTree.addActionListener(this);\r
+ loadAnnotations.addActionListener(this);\r
+ outputFeatures.addActionListener(this);\r
+ outputAnnotations.addActionListener(this);\r
+ selectAllSequenceMenuItem.addActionListener(this);\r
+ deselectAllSequenceMenuItem.addActionListener(this);\r
+ invertSequenceMenuItem.addActionListener(this);\r
+ remove2LeftMenuItem.setLabel("Remove Left");\r
+ remove2LeftMenuItem.addActionListener(this);\r
+ remove2RightMenuItem.setLabel("Remove Right");\r
+ remove2RightMenuItem.addActionListener(this);\r
+ removeGappedColumnMenuItem.setLabel("Remove Empty Columns");\r
+ removeGappedColumnMenuItem.addActionListener(this);\r
+ removeAllGapsMenuItem.setLabel("Remove All Gaps");\r
+ removeAllGapsMenuItem.addActionListener(this);\r
+ viewBoxesMenuItem.setLabel("Boxes");\r
+ viewBoxesMenuItem.setState(true);\r
+ viewBoxesMenuItem.addItemListener(this);\r
+ viewTextMenuItem.setLabel("Text");\r
+ viewTextMenuItem.setState(true);\r
+ viewTextMenuItem.addItemListener(this);\r
+ sortPairwiseMenuItem.setLabel("by Pairwise Identity");\r
+ sortPairwiseMenuItem.addActionListener(this);\r
+ sortIDMenuItem.setLabel("by ID");\r
+ sortIDMenuItem.addActionListener(this);\r
+ sortGroupMenuItem.setLabel("by Group");\r
+ sortGroupMenuItem.addActionListener(this);\r
+ removeRedundancyMenuItem.setLabel("Remove Redundancy...");\r
+ removeRedundancyMenuItem.addActionListener(this);\r
+ pairwiseAlignmentMenuItem.setLabel("Pairwise Alignments...");\r
+ pairwiseAlignmentMenuItem.addActionListener(this);\r
+ PCAMenuItem.setLabel("Principal Component Analysis");\r
+ PCAMenuItem.addActionListener(this);\r
+ averageDistanceTreeMenuItem.setLabel(\r
+ "Average Distance Using % Identity");\r
+ averageDistanceTreeMenuItem.addActionListener(this);\r
+ neighbourTreeMenuItem.setLabel("Neighbour Joining Using % Identity");\r
+ neighbourTreeMenuItem.addActionListener(this);\r
+ statusBar.setBackground(Color.white);\r
+ statusBar.setFont(new java.awt.Font("Verdana", 0, 11));\r
+ statusBar.setText("Status bar");\r
+ outputTextboxMenu.setLabel("Output to Textbox");\r
+ clustalColour.setLabel("Clustalx");\r
+\r
+ clustalColour.addActionListener(this);\r
+ zappoColour.setLabel("Zappo");\r
+ zappoColour.addActionListener(this);\r
+ taylorColour.setLabel("Taylor");\r
+ taylorColour.addActionListener(this);\r
+ hydrophobicityColour.setLabel("Hydrophobicity");\r
+ hydrophobicityColour.addActionListener(this);\r
+ helixColour.setLabel("Helix Propensity");\r
+ helixColour.addActionListener(this);\r
+ strandColour.setLabel("Strand Propensity");\r
+ strandColour.addActionListener(this);\r
+ turnColour.setLabel("Turn Propensity");\r
+ turnColour.addActionListener(this);\r
+ buriedColour.setLabel("Buried Index");\r
+ buriedColour.addActionListener(this);\r
+ userDefinedColour.setLabel("User Defined...");\r
+ userDefinedColour.addActionListener(this);\r
+ PIDColour.setLabel("Percentage Identity");\r
+ PIDColour.addActionListener(this);\r
+ BLOSUM62Colour.setLabel("BLOSUM62 Score");\r
+ BLOSUM62Colour.addActionListener(this);\r
+ avDistanceTreeBlosumMenuItem.setLabel(\r
+ "Average Distance Using BLOSUM62");\r
+ avDistanceTreeBlosumMenuItem.addActionListener(this);\r
+ njTreeBlosumMenuItem.setLabel("Neighbour Joining Using BLOSUM62");\r
+ njTreeBlosumMenuItem.addActionListener(this);\r
+ annotationPanelMenuItem.setLabel("Show Annotations");\r
+ annotationPanelMenuItem.addItemListener(this);\r
+ colourTextMenuItem.setLabel("Colour Text");\r
+ colourTextMenuItem.addItemListener(this);\r
+ overviewMenuItem.setLabel("Overview Window");\r
+ overviewMenuItem.addActionListener(this);\r
+ undoMenuItem.setEnabled(false);\r
+ undoMenuItem.setLabel("Undo");\r
+ undoMenuItem.addActionListener(this);\r
+ redoMenuItem.setEnabled(false);\r
+ redoMenuItem.setLabel("Redo");\r
+ redoMenuItem.addActionListener(this);\r
+ conservationMenuItem.setLabel("by Conservation");\r
+ conservationMenuItem.addItemListener(this);\r
+ noColourmenuItem.setLabel("None");\r
+ noColourmenuItem.addActionListener(this);\r
+ wrapMenuItem.setLabel("Wrap");\r
+ wrapMenuItem.addItemListener(this);\r
+ renderGapsMenuItem.setLabel("Show Gaps");\r
+ renderGapsMenuItem.setState(true);\r
+ renderGapsMenuItem.addItemListener(this);\r
+ findMenuItem.setLabel("Find...");\r
+ findMenuItem.addActionListener(this);\r
+ abovePIDThreshold.setLabel("Above Identity Threshold");\r
+ abovePIDThreshold.addItemListener(this);\r
+ nucleotideColour.setLabel("Nucleotide");\r
+ nucleotideColour.addActionListener(this);\r
+ deleteGroups.setLabel("Undefine Groups");\r
+ deleteGroups.addActionListener(this);\r
+ copy.setLabel("Copy");\r
+ copy.addActionListener(this);\r
+ cut.setLabel("Cut");\r
+ cut.addActionListener(this);\r
+ delete.setLabel("Delete");\r
+ delete.addActionListener(this);\r
+ pasteMenu.setLabel("Paste");\r
+ pasteNew.setLabel("To New Alignment");\r
+ pasteNew.addActionListener(this);\r
+ pasteThis.setLabel("Add To This Alignment");\r
+ pasteThis.addActionListener(this);\r
+ applyToAllGroups.setLabel("Apply Colour To All Groups");\r
+ applyToAllGroups.setState(true);\r
+ applyToAllGroups.addItemListener(this);\r
+ font.setLabel("Font...");\r
+ font.addActionListener(this);\r
+ scaleAbove.setLabel("Scale Above");\r
+ scaleAbove.setState(true);\r
+ scaleAbove.setEnabled(false);\r
+ scaleAbove.addItemListener(this);\r
+ scaleLeft.setEnabled(false);\r
+ scaleLeft.setState(true);\r
+ scaleLeft.setLabel("Scale Left");\r
+ scaleLeft.addItemListener(this);\r
+ scaleRight.setEnabled(false);\r
+ scaleRight.setState(true);\r
+ scaleRight.setLabel("Scale Right");\r
+ scaleRight.addItemListener(this);\r
+ modifyPID.setLabel("Modify Identity Threshold...");\r
+ modifyPID.addActionListener(this);\r
+ modifyConservation.setLabel("Modify Conservation Threshold...");\r
+ modifyConservation.addActionListener(this);\r
+ sortByTreeMenu.setLabel("By Tree Order");\r
+ sort.setLabel("Sort");\r
+ calculate.setLabel("Calculate Tree");\r
+ autoCalculate.addItemListener(this);\r
+ inputText.setLabel("Input from textbox");\r
+ inputText.addActionListener(this);\r
+\r
+ helpMenu.setLabel("Help");\r
+ documentation.setLabel("Documentation");\r
+ documentation.addActionListener(this);\r
+\r
+ about.setLabel("About...");\r
+ about.addActionListener(this);\r
+ seqLimits.setState(true);\r
+ seqLimits.setLabel("Show Sequence Limits");\r
+ seqLimits.addItemListener(this);\r
+ featureSettings.setLabel("Feature Settings...");\r
+ featureSettings.addActionListener(this);\r
+ sequenceFeatures.setLabel("Sequence Features");\r
+ sequenceFeatures.addItemListener(this);\r
+ sequenceFeatures.setState(false);\r
+ annotationColour.setLabel("by Annotation...");\r
+ annotationColour.addActionListener(this);\r
+ invertSequenceMenuItem.setLabel("Invert Sequence Selection");\r
+ invertColSel.setLabel("Invert Column Selection");\r
+ menu1.setLabel("Show");\r
+ showColumns.setLabel("All Columns ");\r
+ showSeqs.setLabel("All Sequences");\r
+ menu2.setLabel("Hide");\r
+ hideColumns.setLabel("Selected Columns");\r
+ hideSequences.setLabel("Selected Sequences");\r
+ invertColSel.addActionListener(this);\r
+ showColumns.addActionListener(this);\r
+ showSeqs.addActionListener(this);\r
+ hideColumns.addActionListener(this);\r
+ hideSequences.addActionListener(this);\r
+ formatMenu.setLabel("Format");\r
+ selectMenu.setLabel("Select");\r
+ newView.setLabel("New View");\r
+ newView.addActionListener(this);\r
+ alignFrameMenuBar.add(fileMenu);\r
+ alignFrameMenuBar.add(editMenu);\r
+ alignFrameMenuBar.add(selectMenu);\r
+ alignFrameMenuBar.add(viewMenu);\r
+ alignFrameMenuBar.add(formatMenu);\r
+ alignFrameMenuBar.add(colourMenu);\r
+ alignFrameMenuBar.add(calculateMenu);\r
+ alignFrameMenuBar.add(helpMenu);\r
+\r
+ fileMenu.add(inputText);\r
+ fileMenu.add(loadTree);\r
+ fileMenu.add(loadAnnotations);\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(outputTextboxMenu);\r
+ fileMenu.add(outputFeatures);\r
+ fileMenu.add(outputAnnotations);\r
+\r
+ if (jalviewServletURL != null)\r
+ {\r
+ fileMenu.add(loadApplication);\r
+ }\r
+\r
+ fileMenu.addSeparator();\r
+ fileMenu.add(closeMenuItem);\r
+\r
+ editMenu.add(undoMenuItem);\r
+ editMenu.add(redoMenuItem);\r
+ editMenu.add(cut);\r
+ editMenu.add(copy);\r
+ editMenu.add(pasteMenu);\r
+ editMenu.add(delete);\r
+ editMenu.addSeparator();\r
+ editMenu.add(remove2LeftMenuItem);\r
+ editMenu.add(remove2RightMenuItem);\r
+ editMenu.add(removeGappedColumnMenuItem);\r
+ editMenu.add(removeAllGapsMenuItem);\r
+ editMenu.add(removeRedundancyMenuItem);\r
+ viewMenu.add(newView);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(menu1);\r
+ viewMenu.add(menu2);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(annotationPanelMenuItem);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(sequenceFeatures);\r
+ viewMenu.add(featureSettings);\r
+ viewMenu.addSeparator();\r
+ viewMenu.add(overviewMenuItem);\r
+ colourMenu.add(applyToAllGroups);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(noColourmenuItem);\r
+ colourMenu.add(clustalColour);\r
+ colourMenu.add(BLOSUM62Colour);\r
+ colourMenu.add(PIDColour);\r
+ colourMenu.add(zappoColour);\r
+ colourMenu.add(taylorColour);\r
+ colourMenu.add(hydrophobicityColour);\r
+ colourMenu.add(helixColour);\r
+ colourMenu.add(strandColour);\r
+ colourMenu.add(turnColour);\r
+ colourMenu.add(buriedColour);\r
+ colourMenu.add(nucleotideColour);\r
+ colourMenu.add(userDefinedColour);\r
+ colourMenu.addSeparator();\r
+ colourMenu.add(conservationMenuItem);\r
+ colourMenu.add(modifyConservation);\r
+ colourMenu.add(abovePIDThreshold);\r
+ colourMenu.add(modifyPID);\r
+ colourMenu.add(annotationColour);\r
+ calculateMenu.add(sort);\r
+ calculateMenu.add(calculate);\r
+ calculateMenu.addSeparator();\r
+ calculateMenu.add(pairwiseAlignmentMenuItem);\r
+ calculateMenu.add(PCAMenuItem);\r
+ calculateMenu.add(autoCalculate);\r
+ this.add(statusBar, BorderLayout.SOUTH);\r
+ pasteMenu.add(pasteNew);\r
+ pasteMenu.add(pasteThis);\r
+ sort.add(sortIDMenuItem);\r
+ sort.add(sortByTreeMenu);\r
+ sort.add(sortGroupMenuItem);\r
+ sort.add(sortPairwiseMenuItem);\r
+ calculate.add(averageDistanceTreeMenuItem);\r
+ calculate.add(neighbourTreeMenuItem);\r
+ calculate.add(avDistanceTreeBlosumMenuItem);\r
+ calculate.add(njTreeBlosumMenuItem);\r
+ helpMenu.add(documentation);\r
+ helpMenu.add(about);\r
+ menu1.add(showColumns);\r
+ menu1.add(showSeqs);\r
+ menu2.add(hideColumns);\r
+ menu2.add(hideSequences);\r
+ formatMenu.add(font);\r
+ formatMenu.add(seqLimits);\r
+ formatMenu.add(wrapMenuItem);\r
+ formatMenu.add(scaleAbove);\r
+ formatMenu.add(scaleLeft);\r
+ formatMenu.add(scaleRight);\r
+ formatMenu.add(viewBoxesMenuItem);\r
+ formatMenu.add(viewTextMenuItem);\r
+ formatMenu.add(colourTextMenuItem);\r
+ formatMenu.add(renderGapsMenuItem);\r
+ selectMenu.add(findMenuItem);\r
+ selectMenu.addSeparator();\r
+ selectMenu.add(selectAllSequenceMenuItem);\r
+ selectMenu.add(deselectAllSequenceMenuItem);\r
+ selectMenu.add(invertSequenceMenuItem);\r
+ selectMenu.add(invertColSel);\r
+ selectMenu.add(deleteGroups);\r
+ }\r
+\r
+ public void setEmbedded()\r
+ {\r
+\r
+ embeddedMenu = new Panel();\r
+ embeddedEdit = new Label("Edit");\r
+ embeddedSelect = new Label("Select");\r
+ embeddedView = new Label("View");\r
+ embeddedFormat = new Label("Format");\r
+ embeddedColour = new Label("Colour");\r
+ embeddedFile = new Label("File");\r
+ embeddedHelp = new Label("Help");\r
+ embeddedCalculate = new Label("Calculate");\r
+ flowLayout1 = new FlowLayout();\r
+ embeddedMenu.setBackground(Color.lightGray);\r
+ embeddedMenu.setLayout(flowLayout1);\r
+ embeddedEdit.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedSelect.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedView.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFormat.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedColour.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedFile.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedHelp.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedCalculate.setFont(new java.awt.Font("Arial", Font.PLAIN, 10));\r
+ embeddedMenu.add(embeddedFile);\r
+ embeddedMenu.add(embeddedEdit);\r
+ embeddedMenu.add(embeddedSelect);\r
+ embeddedMenu.add(embeddedView);\r
+ embeddedMenu.add(embeddedFormat);\r
+ embeddedMenu.add(embeddedColour);\r
+ embeddedMenu.add(embeddedCalculate);\r
+ embeddedMenu.add(embeddedHelp);\r
+ flowLayout1.setAlignment(FlowLayout.LEFT);\r
+ flowLayout1.setHgap(2);\r
+ flowLayout1.setVgap(0);\r
+ embeddedFile.addMouseListener(this);\r
+ embeddedEdit.addMouseListener(this);\r
+ embeddedSelect.addMouseListener(this);\r
+ embeddedView.addMouseListener(this);\r
+ embeddedFormat.addMouseListener(this);\r
+ embeddedColour.addMouseListener(this);\r
+ embeddedCalculate.addMouseListener(this);\r
+ embeddedHelp.addMouseListener(this);\r
+\r
+ fileMenu.remove(closeMenuItem);\r
+ fileMenu.remove(3); // Seperator\r
+\r
+ viewport.applet.setLayout(new BorderLayout());\r
+ viewport.applet.add(embeddedMenu, BorderLayout.NORTH);\r
+ viewport.applet.add(statusBar, BorderLayout.SOUTH);\r
+\r
+ alignPanel.setSize(viewport.applet.getSize().width,\r
+ viewport.applet.getSize().height\r
+ - embeddedMenu.HEIGHT - statusBar.HEIGHT);\r
+\r
+ viewport.applet.add(alignPanel, BorderLayout.CENTER);\r
+ viewport.applet.validate();\r
+\r
+ }\r
+\r
+ PopupMenu filePopup, editPopup, searchPopup,\r
+ viewPopup, formatPopup, colourPopup, calculatePopup, helpPopup;\r
+ MenuItem featureSettings = new MenuItem();\r
+ CheckboxMenuItem sequenceFeatures = new CheckboxMenuItem();\r
+ MenuItem annotationColour = new MenuItem();\r
+ MenuItem invertColSel = new MenuItem();\r
+ Menu menu1 = new Menu();\r
+ MenuItem showColumns = new MenuItem();\r
+ MenuItem showSeqs = new MenuItem();\r
+ Menu menu2 = new Menu();\r
+ MenuItem hideColumns = new MenuItem();\r
+ MenuItem hideSequences = new MenuItem();\r
+ Menu formatMenu = new Menu();\r
+ Menu selectMenu = new Menu();\r
+ MenuItem newView = new MenuItem();\r
+\r
+ public void mousePressed(MouseEvent evt)\r
+ {\r
+ PopupMenu popup = null;\r
+ Label source = (Label) evt.getSource();\r
+ if (source == embeddedFile)\r
+ {\r
+ popup = filePopup = genPopupMenu(filePopup, fileMenu);\r
+ }\r
+ else if (source == embeddedEdit)\r
+ {\r
+ popup = editPopup = genPopupMenu(editPopup, editMenu);\r
+ }\r
+ else if (source == embeddedSelect)\r
+ {\r
+ popup = searchPopup = genPopupMenu(searchPopup, selectMenu);\r
+ }\r
+ else if (source == embeddedView)\r
+ {\r
+ popup = viewPopup = genPopupMenu(viewPopup, viewMenu);\r
+ }\r
+ else if (source == embeddedFormat)\r
+ {\r
+ popup = formatPopup = genPopupMenu(formatPopup, formatMenu);\r
+ }\r
+ else if (source == embeddedColour)\r
+ {\r
+ popup = colourPopup = genPopupMenu(colourPopup, colourMenu);\r
+ }\r
+ else if (source == embeddedCalculate)\r
+ {\r
+ popup = calculatePopup = genPopupMenu(calculatePopup, calculateMenu);\r
+ }\r
+ else if (source == embeddedHelp)\r
+ {\r
+ popup = helpPopup = genPopupMenu(helpPopup, helpMenu);\r
+ }\r
+\r
+ embeddedMenu.add(popup);\r
+ popup.show(embeddedMenu,\r
+ source.getBounds().x,\r
+ source.getBounds().y + source.getBounds().getSize().height);\r
+ }\r
+\r
+ PopupMenu genPopupMenu(PopupMenu popup, Menu original)\r
+ {\r
+ if (popup != null)\r
+ {\r
+ return popup;\r
+ }\r
+ popup = new PopupMenu();\r
+ int m, mSize = original.getItemCount();\r
+ for (m = 0; m < mSize; m++)\r
+ {\r
+ popup.add(original.getItem(m));\r
+ mSize--;\r
+ m--;\r
+ }\r
+\r
+ return popup;\r
+ }\r
+\r
+ public void mouseClicked(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseReleased(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseEntered(MouseEvent evt)\r
+ {}\r
+\r
+ public void mouseExited(MouseEvent evt)\r
+ {}\r
+\r
}\r
git://source.jalview.org / jalview.git / blobdiff